Public policies increasingly promote IUR (Industry-University-Research) collaborations but are often criticized for their suboptimal resource allocation. This study employed textual analysis to extract detailed information on government subsidies for corporate postdoctoral programs from the notes to financial statements of A-share listed companies, thereby examining their actual impact on the national innovation system. The findings revealed that postdoctoral subsidies effectively increase firms’ number of patent applications in the following year, and this effect persisted even after excluding design patents. Additional evidence was provided by distinguishing between specific patent types and accounting treatments. After a series of robustness tests, the above conclusions remain valid. This study further examined the moderating effects of firm-, regional-, and industrial-level factors. The results showed that the positive effect of postdoctoral subsidies on innovation is relatively weaker in contexts where internal controls are ineffective, in regions with preexisting high levels of university resources, or when the firm operates in a labor-intensive industry. Moreover, postdoctoral subsidies enhance a firm’s innovation quality, as reflected by a higher number of patent citations, greater patent generality, and a higher share of exploitative innovations, indicating that the subsidies not only bolster firms’ innovation willingness but also improve innovation quality. Significant spillover effects across the supply chain are also been identified. Overall, these findings offer empirical evidence that government subsidies for corporate postdoctoral programs can effectively stimulate the economy’s innovation vitality, thus will provide a reference for evaluating and continuously optimizing the postdoctoral system.