Guangzhou owns strong economic strength，which ranks 3^rd in the country. However，Guangzhou only stands at the 5^th and 9^th separately in economic competitiveness index and innovation capability. As time going，the economic growth would be weak. Science and technology innovation is inseparable from the cooperation and positive interaction among innovators. Therefore，the research group investigated the government workers，universities faculty，employees and social organizations workers in Guangzhou to analyze the situation of science and technology innovation cooperation. The results showed that there were some problems in government policies，the degree of harmonious cooperation and social intermediary organization system needed to be improved. Considered the actual economic and social development in Guangzhou，with the perspective of polycentric governance theory，the research group proposed a series of countermeasures covering further construction of innovation environment，improving the technological innovation cooperation system and strengthening innovative talents team construction.