Science and technology innovation is the endogenous driving force of a country’s economic development. The improvement of technological innovation capability requires continuous R&D investment, and R&D capital stock is the best indicator to measure the level of continuous R&D investment. Based on the BEA principle, this paper reasonably measures the R&D capital stock of 30 provinces, autonomous regions and cities in mainland China (excluding Tibet), and uses inter-provincial panel data to construct a spatial econometric model to explore the influence mechanism of R&D capital stock on green technology innovation under environmental regulation. The study shows that both environmental regulations and R&D capital stock promote green technology innovation, but a certain intensity of environmental regulations will crowd out R&D input resources, which will have a negative crowding-out effect with the accumulation of R&D capital stock, and thus affect green technology innovation; meanwhile, the effects of R&D capital stock and environmental regulations on green technology innovation in eastern, central and western regions of China show significant regional. The impact of R&D capital stock and environmental regulations on green technology innovation in eastern, central and western China shows significant regional heterogeneity. Therefore, this paper proposes to develop differentiated R&D investment and environmental regulation strategies.