With the development of electronic chip technology and computer science, circuit system is developing continuously toward the miniaturization, intelligentization and highly integration. Under the current of complex electromagnetic environment, the reliability and the stability of information equipment are difficult to meet. The reliability and circuit stability of the system become new challenges in circuit design. This paper proposed an effective method to evolve heterogeneous combination circuit modules, and established a scientific and reasonable heterogeneous circuit evaluation strategy. Through unsimilarity analysis of evolution circuits, some same functions but low correlation structure modules were obtained, which combined heterogeneous circuit that could improve the circuit stability and system fault-tolerant ability. The heterogeneous combination circuit played more stable functions in the complex environment.