Yes it is possible to have multiple master pages for the page contents.
1. Assume you have 2 Master pages (MPage1, MPage2) and 3 Pages (Page1, Page2).
2. First, Select Page1 -> Goto Object tab -> Pagination -> After: goto content area. or Place: goto content area. Select which master page you want for that selected page.
3. Repeat step2 for other following pages.
thanks.
Balaji