Existence of bandgap is an important characteristic of the periodic materials or structures, which has potential use in the development of vibration/sound isolation and frequency filters. By controlling and adjusting the material layout and properties in the periodic microstructure, phonon crystals with special bandgap requirements were designed. In this paper, the optimal design of one-dimensional three-phase phnononic crystals were investigated by genetic algorithm and topology optimization technique and two examples were presented. The results show that three-phase materials can achieve better vibration isolation effect and will reduce the bandgap frequency greatly compared with the two-phase materials, even get up to 99.21% forbidden band. Therefore, it is feasible to use evolutionary algorithm to optimize and design the topology of multi-phase phononic crystals.