As government supports for SMEs’ R&D is increasing every year, the effectiveness of government’s support as well as SMEs’ R&D performance has become important. In this study, the impacts of government R&D support on the qualitative, technological, and economic performance of SMEs was analyzed through a comparative analysis of SMEs with vs. without government R&D support. In [Study 1], the performance difference between SMEs with vs. without government R&D support was compared and analyzed using financial data and survey results of 269 SMEs with government R&D support and 269 non-supported SMEs selected through one-to-one exact matching with supported companies. There was no significant difference between the supported and non-supported companies before participating in the R&D project, however, after the completion of the R&D project, the supported companies showed significantly higher performance. In [Study 2], an analysis was conducted to identify the cause of the performance difference. The result showed that the capabilities and activities of the supported companies affect technical and economic performance by mediating organizational capabilities. This study implies that government R&D support produces results in various aspects, such as the growth of SMEs’ capabilities, in addition to technological and economic performance.