Possessing　independent　intellectual　property　rights,　independent　brand　and　continuous　innovation　ability　is　the　overall　requirements　of　innovative　enterprise　in　our　country.　In　this　paper,　we　take　the　first　batch　innovative　pilot　enterprises　in　Fujian　province　as　the　research　object,　using　the　factor　analysis,　the　paper　discusses　the　internal　factors　of　independent　innovation　in　different　types　of　enterprises,　and　the　paper　has　different　characteristics　analysis　for　all　kinds　of　enterprises.　We　found　that　the　difference　of　internal　factors　influence　of　different　kinks　of　large　enterprises　were　tiny,　in　different　kinds　of　small　and　medium-sized　enterprises,　high-tech　enterprises　and　private　enterprise　the　influence　was　different.　The　conclusion　provides　practical　guides　for　local　government　to　further　promote　innovative　enterprise　pilot　job.