Innovative enterprise refers to the enterprise that is outstanding independent intellectual property rights, relying on technological innovation to obtain market competitive advantage, competitive and sustainable development in the international market.As the main body of innovation, innovative enterprises are the new force for the implementation of innovation driven strategy. An index system is constructed to analyze the influencing factors of independent innovation of innovative enterprises in Taizhou by means of interview and research, expert interview and literature review.The index system includes four secondary index systems: talent investment, capital investment, government expenditure and innovation management. Each secondary index system includes four index systems respectively, and finally 16 tertiary index systems are formed.Then,analytic hierarchy process (AHP) is used to analyze and determine the impact of each index on the independent innovation of innovative enterprises. According to the empirical results,the strategies and development paths are put forward to improve the independent innovation ability of innovative enterprises from the aspects of talent cultivation, scientific and technological innovation platform construction, intellectual property protection, enterprise investment and financing.