When your native query is based on joins, in that case you can get the result as list of objects and process it.
one simple example.
@Autowired
EntityManager em;
String nativeQuery = "select name,age from users where id=?";
Query query = em.createNativeQuery(nativeQuery);
query.setParameter(1,id);
List<Object[]> list = query.getResultList();
for(Object[] q1 : list){
String name = q1[0].toString();
//..
//do something more on
}