Intellectual capital plays different roles in innovation performance in different life cycle stages of enterprise. According to the panel data model and the modified value added intellectual coefficient and the panel data of the Chinese listed companies from 2007 to 2012, this paper empirical study of the relationship between the intellectual capital and innovation performance of the enterprise in different life cycle stages. The results show that the total investment intellectual capital of enterprise has a significant positive effect on innovation performance in the life cycle stages. Human capital investment in the life cycle phase has little impact on innovation performance, even a negative role in growth period. Process capital investment, relational capital investment and innovation capital investment plays a significantly positive role of innovation performance respectively in the life cycle. In the growth and decline stages, innovation capital investment effect coefficient is larger than others. In the mature stages, relationship capital investment effect coefficient is larger than others. The conclusion of the research provides empirical basis of innovation performance and investment decision-making reference for enterprises in different life cycle stages.