Something that's described as inner is at the center or interior. You inner ear, for example, is the part of your ear that you can't see.
The inner pocket of your winter coat is the one closest to your body, and an inner courtyard is usually surrounded by at least one surrounding outer courtyard. Inner strength is the kind that comes from deep within your essential self, and an "inner circle" is a small privileged group of people with special access to information or influence. The "inner city" usually means the poorest section of a big city.