Difference between SHA256withRSA and SHA256 then RSA

******Without BouncyCastle I adjusted your solution folowing the mkl's answer steps******

import java.security.MessageDigest;
import java.security.PrivateKey;
import java.security.Signature;
import java.security.interfaces.RSAPrivateCrtKey;

import sun.security.rsa.RSACore;
import sun.security.rsa.RSAPadding;
import sun.security.util.DerOutputStream;
import sun.security.util.DerValue;
import sun.security.x509.AlgIdDSA;
import sun.security.x509.AlgorithmId;

public class MySHA256 {

    public static void main(String[] args) throws Exception {

        String s = "1234";
        MessageDigest messageDigest = MessageDigest.getInstance("SHA-256");
        messageDigest.update(s.getBytes());
        byte[] outputDigest = messageDigest.digest(); 
        //compute SHA256 first
        DerOutputStream out = new DerOutputStream();
        new AlgorithmId(AlgIdDSA.SHA256_oid).encode(out);
        out.putOctetString(outputDigest);
        DerValue result = new DerValue(DerValue.tag_Sequence, out.toByteArray());
        byte[] encoded = result.toByteArray();      
        //sign SHA256 with RSA
        PrivateKey privateKey = Share.loadPk8("D:/key.pk8");
        RSAPrivateCrtKey pkRSA = (RSAPrivateCrtKey)privateKey;
        int keySize = RSACore.getByteLength(pkRSA);
        RSAPadding padding = RSAPadding.getInstance(RSAPadding.PAD_BLOCKTYPE_1, keySize, null);
        byte[] padded = padding.pad(encoded);
        byte[] signed = RSACore.rsa(padded, pkRSA, true);
        System.out.println(bytesToHex(signed));


        //compute SHA256withRSA as a single step
        Signature rsaSha256Signature = Signature.getInstance("SHA256withRSA");
        rsaSha256Signature.initSign(privateKey);
        rsaSha256Signature.update(s.getBytes());
        byte[] signed2 = rsaSha256Signature.sign();
        System.out.println(bytesToHex(signed2));
    }

    public static String bytesToHex(byte[] bytes) {
        final char[] hexArray = "0123456789ABCDEF".toCharArray();
        char[] hexChars = new char[bytes.length * 2];
        for ( int j = 0; j < bytes.length; j++ ) {
            int v = bytes[j] & 0xFF;
            hexChars[j * 2] = hexArray[v >>> 4];
            hexChars[j * 2 + 1] = hexArray[v & 0x0F];
        }
        return new String(hexChars);
    }



}

The difference

The difference between signing with "SHA256withRSA" and computing the SHA256 hash and signing it with "RSA" (= "NONEwithRSA") is foremost that in the former case the calculated SHA-256 hash value is first encapsulated in a DigestInfo structure

DigestInfo ::= SEQUENCE {
    digestAlgorithm DigestAlgorithm,
    digest OCTET STRING
}

before being padded and then encrypted while in the latter case the naked SHA256 hash value is padded and encrypted.

If they are different, is there a way to modify the method 2 so that both methods give the same output?

First and foremost you will have to encapsulate the hash value in a DigestInfo structure before signing using "NONEwithRSA".

RFC 3447 Section 9.2 helps here by stating in Note 1 that

1. For the six hash functions mentioned in Appendix B.1, the DER
   encoding T of the DigestInfo value is equal to the following:
   ...
   SHA-256: (0x)30 31 30 0d 06 09 60 86 48 01 65 03 04 02 01 05 00
                04 20 || H.

Making it work

In response to the section above the OP updated his question with the updated code. Unfortunately, though, it did not yet work for him. Thus,

The OP's code

I executed the OP's code (SignInSteps.java). As he didn't provide the private key, I used a test key of my own (demo-rsa2048.p12). The result:

GreenhandOriginal:
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

GreenhandUpdated:
method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
method 2: 4B9ECA6DD47C1B230D972E7DA026165F1CE743EC96825E4C13DFE2C6437FE673A13CA622047EE7D2F7C5280198D81550A1CBD17F8E8A3C4C2D53A746FA6464AA5194FC2782527B014F017008D89BB2C80B7FA367C74FE01369986B56BCE7DC573A11ED884511F0CB12160CA5E42D488451AA8961BF5A9F71E6A5E89F19BC8EFAC26DDE989A0369667EE74372F6E558887FE2561EA926B441AB8F0FD3DEDD608A671011313372084B059CAD7E4807AC852C0873C57F216349422771C089678BAC3021D054C4427EADE70219E251617B83E68640DD7D03C3F99E47F79EB71C124F59EDEA724496A4552F2E9E1F90DDE550745E85483D823F146982C6D2008FE9AA

Thus, in contrast to the OP's observations, signatures equal in case of the updated code.

Not assuming copy&paste errors, there still might be other differences involved.

The environment

I tested using Java 8 (1.8.0_20) with unlimited jurisdiction files added and BouncyCastle 1.52, 1.49, and 1.46 (with a small test code modification due to the BC API changes).

The OP mentioned in a comment:

The Java is JRE 8 update 66. The BouncyCastle is bcprov-jdk15on-153.jar.

Thus I updated Java, still no difference.

Then I updated BouncyCastle to 1.53. And indeed, suddenly the results differed:

GreenhandOriginal:
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

GreenhandUpdated:
method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
method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

Interestingly only the value for method 1 in the updated code differs. Thus, I looked at the intermediary objects in that case

[BC 1.52]
hash: 03AC674216F3E15C761EE1A5E255F067953623C8B388B4459E13F978D7C846F4
algo: 2.16.840.1.101.3.4.2.1
info: 3031300D06096086480165030402010500042003AC674216F3E15C761EE1A5E255F067953623C8B388B4459E13F978D7C846F4

[BC 1.53]
hash: 03AC674216F3E15C761EE1A5E255F067953623C8B388B4459E13F978D7C846F4
algo: 2.16.840.1.101.3.4.2.1
info: 302F300B0609608648016503040201042003AC674216F3E15C761EE1A5E255F067953623C8B388B4459E13F978D7C846F4

Thus, BouncyCastle 1.53 encodes the DigestInfo object differently! And the encoding in 1.52 (and below) is the one expected by the RFC 3447 Section 9.2.

Looking at the ASN.1 dumps one sees that BC 1.52 encodes the AlgorithmIdentifier as

 2  13:   SEQUENCE {
   <06 09>
 4   9:     OBJECT IDENTIFIER sha-256 (2 16 840 1 101 3 4 2 1)
      :       (NIST Algorithm)
   <05 00>
15   0:     NULL
      :     }

while BC 1.53 creates

 2  11:   SEQUENCE {
   <06 09>
 4   9:     OBJECT IDENTIFIER sha-256 (2 16 840 1 101 3 4 2 1)
      :       (NIST Algorithm)
      :     }

So in 1.53 the algorithm parameters are missing altogether. This suggests changing the line

AlgorithmIdentifier sha256Aid = new AlgorithmIdentifier(NISTObjectIdentifiers.id_sha256, null);

to

AlgorithmIdentifier sha256Aid = new AlgorithmIdentifier(NISTObjectIdentifiers.id_sha256, DERNull.INSTANCE);

and suddenly it works with BouncyCastle 1.53, too, the values for method 1 and method 2 coincide! ;)

TL;DR

Don't use null as the SHA-256 parameters when instantiating the AlgorithmIdentifier, use DERNull.INSTANCE instead.

How did I...

In a comment the OP indicated that he'd like to know more about

  1. how do you inspect the intermediate object of BouncyCastle and
  2. how do you produce the ASN.1 dumps.

So...

... inspect the intermediate object

Quite simple. First I split up the line

rsaSignature.update(di.toASN1Primitive().getEncoded());

in the updated code as

byte[] encodedDigestInfo = di.toASN1Primitive().getEncoded();
rsaSignature.update(encodedDigestInfo);

and then added console outputs

System.out.println("    hash: " + bytesToHex(outputDigest));
System.out.println("    algo: " + sha256Aid.getAlgorithm());
System.out.println("    info: " + bytesToHex(encodedDigestInfo));

Finally I executed the code with the different BouncyCastle versions.

... produce the ASN.1 dumps

There is a well-known utility called dumpasn1 by Peter Gutmann which has become the kernel of many command line and GUI tools for creating and displaying ASN.1 dumps. I currently happen to use GUIdumpASN-ng.

In the case at hand I saved the contents of the byte[] encodedDigestInfo to a file (which can be done using e.g. Files.write) and opened these files in GUIdumpASN-ng.