In the context of global economic integration，regional innovation capacity has become an important symbol of the decisive factors of the regional economy to gain international competitive advantage and the regional economic participants reflect their competitive advantage. We compare the regional innovation capacity among Guangzhou，Beijing，Tianjin，Shanghai and Chongqing by Factor Analysis Method. In order to reveal the strengths and gaps in the field of regional innovation，we analyze the innovation capacity from regional innovation strength，regional innovation contribution and regional innovation competitiveness.