Hibernate 5.6 has huge performance issues after upgrade of Java, Spring &Hibernate versions. Why?

Upgraded a java project which was on Java 8 + spring 4.0 + hibernate 3.3 to java 11 + spring 5.3 + hibernate 5.6 . After the upgrade the hibernate select queries become very slow. When there’re many results for a select query then the hibernate 5.6 is taking a lot of time compared to hibernate 3.3. What could be the reason?

Without seeing the entity model, queries and a flame graph for both executions, it’s very hard to say. Between Hibernate ORM 3.3 and 5.6 lots of things happened, the releases are many years apart and at this point, even ORM 5.6 is old and only receives limited support.
You missed the moment in time when people still had good knowledge about such potential issues. I don’t think there is anyone around who can really help you at this point. You will have to investigate this yourself.