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.