How to modify a huge XML file by StAX?

Try this

    XMLInputFactory inFactory = XMLInputFactory.newInstance();
    XMLEventReader eventReader = inFactory.createXMLEventReader(new FileInputStream("1.xml"));
    XMLOutputFactory factory = XMLOutputFactory.newInstance();
    XMLEventWriter writer = factory.createXMLEventWriter(new FileWriter(file));
    XMLEventFactory eventFactory = XMLEventFactory.newInstance();
    while (eventReader.hasNext()) {
        XMLEvent event = eventReader.nextEvent();
        writer.add(event);
        if (event.getEventType() == XMLEvent.START_ELEMENT) {
            if (event.asStartElement().getName().toString().equalsIgnoreCase("book")) {
                writer.add(eventFactory.createStartElement("", null, "index"));
                writer.add(eventFactory.createEndElement("", null, "index"));
            }
        }
    }
    writer.close();

Notes

new FileWriter(file, true) is appending to the end of the file, you hardly really need it

equalsIgnoreCase("book") is bad idea because XML is case-sensitive

Well it is pretty clear why it behaves the way it does. What you are actually doing is opening the existing file in output append mode and writing elements at the end. That clearly contradicts what you are trying to do.

(Aside: I'm surprised that it works as well as it does given that the input side is likely to see the elements that the output side is added to the end of the file. And indeed the exceptions like Evgeniy Dorofeev's example gives are the sort of thing I'd expect. The problem is that if you attempt to read and write a text file at the same time, and either the reader or writer uses any form of buffering, explicit or implicit, the reader is liable to see partial states.)

To fix this you have to start by reading from one file and writing to a different file. Appending won't work. Then you have to arrange that the elements, attributes, content etc that are read from the input file are copied to the output file. Finally, you need to add the extra elements at the appropriate points.

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And is there any possibility to open the XML file in mode like RandomAccessFile, but write in it by StAX methods?

No. That is theoretically impossible. In order to to be able to navigate around an XML file's structure in a "random" file, you'd first need to parse the whole thing and build an index of where all the elements are. Even when you've done that, the XML is still stored as characters in a file, and random access does not allow you to insert and remove characters in the middle of a file.

Maybe your best bet would be combining XSL and a SAX style parser; e.g. something along the lines of this IBM article: http://ibm.com/developerworks/xml/library/x-tiptrax