Abstract: Based on the framework of Multi-level perspectives (MLP), this paper proposes the evolution model of innovation ecosystem, and divides the evolution of innovation ecosystem into three periods, which are technology protection, market selection, and competition diffusion, combining the characteristics of technology niche, market niche, and social technology regime. Then the effectiveness of the model is verified with the case study on the innovation ecosystem of new energy public transportation in Shenzhen. The results show that the innovation ecosystem evolves orderly through the stage of technology protection, market selection, competition diffusion; the developing strategies of focal firms make decisive effect on the development of the innovation ecosystem; policy support plays an crucial supporting role to the evolution of the innovation ecosystem; the evolution of innovation ecosystem is the synergism and co-operative results of these actors in the system. The results are important for deepening and developing the strategy of new energy transportation.