As a strategic emerging industry, the new energy industry can promote green and low-carbon development. While the impact of environmental regulations on green innovation has been widely discussed, the underlying mechanism of heterogeneous environmental regulations affecting green innovation in new energy companies has not yet attracted attention. The dataset of this study covers the panel data of A-share new energy companies listed in Shanghai and Shenzhen from 2012 to 2020. The two-way fixed-effect model is used to draw the conclusion that command-and-control environmental regulation(CCR) and market investment-oriented environmental regulation(MIR) promote the green innovation of new energy firms. Compared with CCR, MIR exerts a stronger and more significant incentive impact on the green innovation of firms. Besides, firms’ investment in R&D has a partial mediation effect between CCR and green innovation, and firms’ production cost has a partial mediation effect between MIR and green innovation. Furthermore, through the heterogeneity test of firms, the results indicate that both types of environmental regulations substantially encourage the green innovation of large-scale and state-owned firms. Therefore, the government should give full play to the incentive effects of environmental regulations, select environmental regulation tools scientifically and formulate the optimal combination of environmental regulations.