Countries with low technology levels have narrowed the technological gap with developed countries through continuous and strategic R&D (Research and Development) investment. However, inefficient R&D with a low performance is among the chronic problems of these countries. While factors such as budget, manpower, and operational process influence R&D innovation output (IO), the autonomous R&D climate and commitment in projects are also essential. This study analyzes the effects of professional autonomy (PA) and project commitment (PC) on the performance of 1,087 government-funded R&D projects in Korea. Our results indicate that PA improves R&D IO in the research planning stage. Additionally, PC has a negative effect on R&D IO, but there are positive moderating effects between both large firm involvement and project duration and R&D performance. Our study on research autonomy and commitment presents policy implications for improving the efficiency of R&D projects in countries that are transitioning from catching up to leading in R&D.