This paper analysis the cross-section data of innovative enterprises (pilot) in Fujian Province of China. Firstly, we did stepwise regression to the overall sample and established a model of production function about innovation. Secondly, we divided the sample into 3 clusters through k-mean cluster, and established the model of production function for each cluster. Thirdly, we compared the 4 models and try to causation of differences of them. The main conclusion includes three aspects, one is that the innovative enterprise(pilot) in Fujian province of China are all increasing returns to scale, two is that we found differences between innovative enterprises (pilot) in the 3 clusters, three is we proved the necessity of differential policy for the local government in order to further promote the regional innovation.