In this research, we focus on the collaboration efficiency that arises from the research and development (R&D) efforts of small and medium-sized enterprises (SMEs) in Korea. Many research studies insist on the importance of the effectiveness of collaboration; however, only a few focus on the efficiency. Thus, this study investigates the effect of collaboration and collaboration type in terms of innovation efficiency for SMEs. First, we evaluate and compare the innovation efficiency of collaboration by applying data envelopment analysis-based global Malmquist productivity analysis. Then, we characterized the collaboration typology through cluster analysis and analyzed the features of the configured collaboration types. Finally, we analyze innovation efficiency to evaluate the performance of the collaboration types. More specifically, we examine the stepwise effect of collaboration for the phases of innovation, and we confirmed that collaboration had different effects on R&D and commercialization. Throughout this research, we found that DEA can be applied to innovation management area in the sense of developing collaborated innovation strategies and collaboration modes, in fact we confirm that the innovation efficiency resulting from DEA may generate suitable managerial strategies for collaboration. Also, four collaboration types identified in this study also showed considerably different innovation characteristics and efficiency. In addition, the results imply that differentiated collaboration strategy is required considering the technological intensity.