A PhraseQuery matches a particular sequence of terms, while a MultiPhraseQuery gives you an option to match multiple terms in the same position. For example, MultiPhrasQuery supports a phrase such as humpty (dumpty OR together) in which it matches humpty in position 0 and dumpty or together in position 1.
Here is a code snippet to demonstrate both Query types:
PhraseQuery query = new PhraseQuery();
query.add(new Term("content", "humpty"));
query.add(new Term("content", "together"));
MultiPhraseQuery query2 = new MultiPhraseQuery();
Term[] terms1 = new Term[1];terms1[0] = new Term("content", "humpty");
Term[] terms2 = new Term[2];terms2[0] = new Term("content", "dumpty");
terms2[1] = new Term("content", "together");
query2.add(terms1);
query2.add(terms2);