Innermost things are located as far as possible inside or closest to the middle. The innermost part of a jelly doughnut is the where you'll find the jelly.
The innermost room at your school — or the room at the very center — might be the library, and an Alaskan's innermost layer of clothing in the winter is probably her long underwear. Another way to use innermost is to mean "most intimate or private," such as your innermost beliefs, thoughts, or dreams. In Middle English, there was also an innermore.