He was indeed a master of counterpoint. However the original work on counterpoint was written by Johann Fux. If you want more information on counterpoint try wikipedia.com. The subject is too vast to cover in such vague terms.

He composes a specific melody line with a specific rhythm for one instrument voicing, then he composes a second melody that differs (or counters) from the first in both rhythm and melody. Although they counter, they compliment each other. Bach definately is the epitome of counterpoint.