Brian means that his mind and body are working in perfect unison. There is no longer a disconnect between thoughts and actions. His mind registers a stimulus of some kind, and his body instantly responds without being told to do so by his conscious mind.
The full quote is as follows:
None of that used to be in Brian and now it was a part of him, a changed part of him, a grown part of him, and the two things, his mind and his body, had come together as well, had made a connection with each other that he didn't quite understand. When his ears heard a sound or his eyes saw a sight his mind took control of his body. Without his thinking, he moved to face the sound or sight, moved to make ready for it, to deal with it.
The quote appears in chapter 11 of Gary Paulsen's Hatchet. The chapter mainly focuses on how Brian's mind and body are changing. Physically, he is becoming much more lean and tan. That makes sense. He's surviving outside with a minimal calorie intake. The changes in his mind are more important though. Not only is Brian's environment changing his body, but it is also changing his mind. He sees nature differently. He has started to see the meaning in certain natural events. For example, the chapter goes on to explain that Brian could see ripples in the water, and he knew what kind of wind was needed to make that particular ripple. Because his mind is more in tune with his environment, his body is also better prepared to respond to that environment.