Abstract: Purpose/Significance Understanding the impact mechanism of R&D investment and heterogeneous regional economic and industrial environment on regional innovation quality is an important basis for effective allocation of innovation resources. Design/Methodology Based on the comprehensive evaluation of regional innovation quality, this paper adopts the panel regression model to analyze the impact of four types of R&D investment on regional innovation quality. Given the regional economic and industrial environment as the threshold variable, the panel threshold regression model is applied to explore non-linear relationship between R&D investment and regional innovation quality. Findings/Conclusions Enterprises’ R&D investment could promote regional innovation quality with a significant short-term effect. The governmental R&D investment in the short term has a significant negative impact, and R&D investment from foreign and other sources produces diverse impact. Regional economic development, industrial structure, property right structure and the degree of opening up have remarkable differential effects. R&D investment strategies should be formulated based on the heterogeneity of regional economic and industrial environment, in order to promote regional innovation quality more effectively.