Using the data of UniversityIndustry (UI) collaboration with MOE& MOST in Guangdong province, the paper discusses the relations among investment form separate sources and its impact on innovation performance. The results show that from the structure of R&D funds in UI collaboration, investment from government plays a better leverage in guiding enterprise to increase R&D investment, and the mount of social funds used for R&D cuts no figure and funds at the disposal of enterprises play a dominant role in raising technology ability and acquiring competitive advantage. Enterprise’s leverage effect caused by public investment in R&D activities exceeds its crowdout effect. The need of SMEs partaking in UI collaboration is much stronger, but its cooperation outcomes show less effective compared with large enterprises. Export orientation shows indistinctive promotion for cooperative enterprise absorbing foreign technology spillover.