Based on the empirical analysis of panel data on new energy listed companies in China, the relationships among government subsidies, enterprise research and development input (R&D input), and firm performance are explored to measure the impact of government subsidies on firm performance and the mediation mechanism of R&D input. In addition, the effects of the moderation variables of regional characteristics and state ownership are measured from the enterprise heterogeneity perspective. The results show that government subsidies have a positive promoting effect on R&D input; R&D input has a two-year lag positive effect on firm performance; government subsidies have a two-year lag positive effect on firm performance through the mediation role of R&D input. Regional characteristics and enterprise properties moderate the effect of government subsidies on firm performance. Government subsidies have a greater positive effect on firm performance in the eastern coastal areas than they do in mid-west coastal areas, and there is a crowding-out effect on the mid-west coastal areas. Government subsidies have a greater positive effect on the performance of non-state-owned enterprises than they do on state-owned enterprises. Suggestions are provided for the government to adjust subsidy policy and improve the performance of new energy enterprises.