Based on the perspective of the regional innovation system, this study constructs an analytical framework for the influence of government R&D funding on regional innovation quality and uses 283 Chinese cities as research samples to empirically test the influence of government R&D funding methods such as subsidies and tax preferences on regional innovation quality by the spatial Durbin model. According to the study, China’s regional innovation quality has a positive spatial correlation. Subsidies can improve regional innovation quality, which is mainly (...) realized by increasing the input of innovation resources from local direct innovation subjects, attracting the inflow of innovation resources from neighboring areas, and increasing the innovation support from local indirect innovation subjects. Besides, spatial competition for subsidies makes it beneficial to improve the regional innovation quality in neighboring regions, while the promotion effect of tax preferences is not significant. When considering the heterogeneity of the city location and administrative hierarchy, it shows that the government R&D funding cannot improve the innovation quality of the Eastern cities and higher-administrative-hierarchy cities, while it can improve that of the Middle and Western cities and general-administrative-hierarchy cities. Furthermore, government R&D funding widens the gap of regional innovation quality, which may be related to the existing “insufficient intervention” and “excessive intervention” of government R&D funding. This study provides insights into the implementation of R&D funding by the government to promote the development of regional innovation quality. (shrink)