Innovative　pilot　enterprise　is　very　important　for　regional　innovation　system　construction,　and　it　can　not　be　ignored.　This　article　chose　innovative　(pilot)　enterprises　in　Fujian　province　as　research　sample,　analyzed　the　distributional　characteristics　of　each　output　and　synthetic　output　performance,　using　multiple　regression　model　to　analyze　relevant　factors.　We　concluded　that　technology　research　and　development　institutions,　R&D　personnel,　Staff　educational　and　training　expenditure,　innovation　incentive　mechanism　have　significant　influence　on　output　performance,　this　provides　a　practical　guidence　for　local　government　to　further　promote　innovative　pilot　enterprise.