How to copy HashMap (not shallow copy) in Java

This does need iteration unfortunately. But it's pretty trivial with Java 8 streams:

mapCopy = map.entrySet().stream()
    .collect(Collectors.toMap(e -> e.getKey(), e -> List.copyOf(e.getValue())))

You're right that a shallow copy won't meet your requirements. It will have copies of the Lists from your original map, but those Lists will refer to the same List objects, so that a modification to a List from one HashMap will appear in the corresponding List from the other HashMap.

There is no deep copying supplied for a HashMap in Java, so you will still have to loop through all of the entries and put them in the new HashMap. But you should also make a copy of the List each time also. Something like this:

public static HashMap<Integer, List<MySpecialClass>> copy(
    HashMap<Integer, List<MySpecialClass>> original)
{
    HashMap<Integer, List<MySpecialClass>> copy = new HashMap<Integer, List<MySpecialClass>>();
    for (Map.Entry<Integer, List<MySpecialClass>> entry : original.entrySet())
    {
        copy.put(entry.getKey(),
           // Or whatever List implementation you'd like here.
           new ArrayList<MySpecialClass>(entry.getValue()));
    }
    return copy;
}

If you want to modify your individual MySpecialClass objects, and have the changes not be reflected in the Lists of your copied HashMap, then you will need to make new copies of them too.

Serialize to json and deserialize afterwards:

Map<String, Object> originalMap = new HashMap<>();
String json = new Gson().toJson(originalMap);
Map<String, Object> mapCopy = new Gson().fromJson(
    json, new TypeToken<Map<String, Object>>() {}.getType());

For special classes you might need to write a custom deserializer.

Just use Apache Commons Lang - SerializationUtils.clone();

Something like these:

    Map<String, List<MySpecialClass>> originalMap = new HashMap();
    HashMap<String, List<MySpecialClass>> deepCopy = SerializationUtils.clone(new HashMap<>(originalMap));

Also make sure MySpecialClass implements Serializable interface.

public class MySpecialClass implements Serializable{}