The purpose of this study is to empirically examine the role of manufacturing in improving innovation efficiency of emerging economies. Emerging economies are developing innovations to promote their industries toward high-technology sectors to facilitate global competitiveness. Nevertheless, the role of manufacturing is often neglected, which can result in low efficiency in the innovation process. This study constructed a three-stage innovation model that consists of human capital cultivation, manufacturing development, and innovation production to stress and verify the importance of manufacturing. The experimental results suggest that manufacturing development was a key factor affecting innovation efficiency. A performance improvement strategy map was provided to improve each country's innovation efficiency.