Sustainable innovation is an important factor for enterprises to obtain core competitiveness in modern society, and only continuous R&D investment can ensure the smooth progress of enterprise innovation. Therefore, this study uses the post-subsidy data of enterprise R&D investment released by Hangzhou Science and Technology Bureau to explore the influencing factors of R&D investment and its sustainability by Chinese high-tech enterprises. In contrast to previous research which mainly focused on the pre-subsidy, this study focuses on the post-subsidy policy of R&D investment sustainability. Empirical analysis methods, such as cross-sectional linear regression and the propensity-score-matching method, were used to draw the following conclusions: (1) The quantity and sustainability of R&D investment of enterprises are obviously unbalanced among regions. Regions where high-tech enterprises are concentrated have higher levels of R&D investment and sustainability than other regions. (2) Under different scales, there are significant differences in the amount and sustainability of R&D investment. Large enterprises have stronger R&D investment strength, while small enterprises have stronger R&D investment willingness. However, the effect of scale on R&D investment will be reduced by regional factors. (3) The evaluation of high-tech enterprises and the enterprises’ R&D investments affect each other. (4) The sustainability of enterprise R&D investment will be affected by enterprise heterogeneity factors, and in turn, the sustainability of enterprise R&D investment will also affect the amount of enterprise R&D investment. Based on the results, the study provides suggestions for the government to make more targeted policies.