Science-technology-based small and medium-sized enterprises(S & T SMEs), are the carrier of technological achievements transformation and innovation realization. Clustering innovation presents a highly efficient way for development of S & T SMEs. In this paper, based on theoretical analysis, the innovation effect produced by S & T SMEs' clustering innovation is confirmed. Then, the primary influencing factors on clustering innovation effect are identified and fundamental hypotheses are put forward afterwards through theoretical analysis. At last, related hypotheses put forward in this paper are verified through questionnaire investigation and structural equation model, which provides SMEs with decision basis when choosing a proper path to improve the ability of technological innovation.