Abstract: This paper is determined to explore the relationship between knowledge division, knowledge synergy and innovation performance including technical effect and scale effect. Various data sources including R&D inputs and innovation results during 2000-2014 of University, research institutes and enterprises, are used to measure the innovation performance by the method of DEA, to make an empirical study by the model of tobit. It has been found that: (1)knowledge division is positively related to the technical effect, negatively correlated with the scale effect, and exhibit a reverse “U” relationship with the innovation performance;(2) knowledge synergy, technology effect, scale effect and innovation performance are positively correlated;(3) knowledge synergy can enhance the positive marginal contribution of knowledge division to the technology effect, and reduce the negative marginal contribution of knowledge division to the scale effect, which makes the marginal contribution of knowledge division to innovation performance increasing.