Taking China provincial-level data during 2003–2017 as the basic space-time unit, this research applies the Moran index and spatial econometric model to analyze the spatial pattern change trend and spillover effects of regional innovation output. The results show that, first, provincial innovation outputs mainly concentrate in the coastal economic belt and Yangtze economic zone. Second, there is a correlation in space for provincial innovation output, and the growth rate of provincial innovation output has a positive spillover effect. The rate of conditional β-convergence is 3.926%, and the half-life cycle of convergence is 17.665 years. Third, environmental regulations have pushed the development of regional innovation to some extent. Fourth and finally, regional innovation input and its spillover effects impact the level of regional innovation output. Innovation output, environment regulation, and R&D internal expenditure are the main paths for innovation’s spillover effect.