On the basis of investigation and interview, so many affect factors were found out, and according to the research on innovation theory, the affect factors of technology innovation in Marine pharmaceutical enterprises in Zhejiang province were identified as human resources, Marine science and technology policy, financing environment, infrastructure, and Marine technology platform, Marine cultural environment, marketization degree, natural resources, etc. The relationship between the affect factors was clarified, and the impact on the Marine technology innovation was analyzed. a data envelopment analysis mode (DEA) was constructed to study the technology innovation performance evaluation. On the basis of the evaluation of Marine science and technology innovation ability of Zhejiang province, the feasible suggestions to promote its development were put forward.