Small and medium-sized enterprises (SMEs) play a pivotal role in the national economy. In particular, the manufacturing sector accounts for a substantial share of domestic employment, exports, and domestic demand. Consequently, the manufacturing capabilities of SMEs, specifically their product and process innovation capabilities, are critical determinants of corporate survival, and the government supports these firms through a variety of institutional schemes. This study analyzes the moderating effect of government support systems on the relationship between the performance of product and process innovation and innovation persistence. Data from the 2024 Manufacturing Sector of the Korean Innovation Survey (KIS), conducted by the Science and Technology Policy Institute (STEPI), were utilized, with a total of 1,850 SMEs selected as the final sample for analysis. The results indicate that innovation activities inherently contribute to maintaining innovation persistence. Furthermore, government support generally demonstrated a positive moderating effect on process innovation, with financial support showing a particularly significant impact. However, the interaction between process innovation and technical support was not found to be statistically significant. This study contributes to the literature by demonstrating that the expected effects of government support for innovation activities may vary depending on the support type. Moreover, the findings offer practical implications for firms in formulating strategies to leverage external support effectively.