Based on the theoretical framework of “technology-organization-environment”, the influencing factors of innovation performance improvement of new energy enterprises were constructed. Taking 141 listed new energy enterprises as samples, fuzzy set qualitative comparative analysis method was used to explore the configuration path of innovation performance improvement of new energy enterprises. The results indicate that R&D capability, innovation resources, innovation consciousness of senior management team, firm scale, market competition and government support are not independent influences but the results of multi-factor synergies. Three configuration paths to improve the innovation performance of new energy enterprises are the “technology-environment” logic and “technology-organization-environment” logic led by the consequent innovation path, and the “organization-environment” logic led by the potential innovation path. There is a complementary and substitutive relationship among innovation resources, R&D capabilities and executive team innovation consciousness, and R&D capabilities have a more significant impact on the innovation performance of new energy enterprises than innovation resources.