How to do multiple filter query in Elasticsearch using Java?

You can use the terms query instead of multiple term queries:

BoolQueryBuilder boolQuery = QueryBuilders.boolQuery()
                .must(QueryBuilders.simpleQueryStringQuery(query).field("newContent").field("T"))
                .filter(QueryBuilders.termsQuery(Collection, "abc", "xyz"));
                                          ^                    ^      ^
                                          |                    |      |
                                    use termsQuery      with multiple values

UPDATE

I'm surprised your code compiles at all because you're missing some closing parenthesis, just rewrite your query like this and it should work:

    BoolQueryBuilder boolQuery = QueryBuilders.boolQuery()
            .must(QueryBuilders.simpleQueryStringQuery(query).field("newContent").field("T"))
            .filter(QueryBuilders.termQuery(Collection[0], "true"))
            .filter(QueryBuilders.termQuery(Collection[1], "true"));