In order to solve the problems that how to mine and express classification knowledge and rules in compatibility of prescription, this paper introduces a new theory of formal concept analysis (FCA), and realizes the compatibility of prescription knowledge mining. Meanwhile, the prescription drugs of reverting yin disease treatment in Treatise on febrile diseases are selected to apply the FCA theory to mine the compatibility of prescription. The result shows that complete knowledge which is related to prescription can be obtained from the attribute partial order chart, therefore it has been proved that the theory of FCA provides a new method to discovery the new knowledge of prescription of TCP.