Nowadays, one of the main challenges facing green innovation management is how to enhance the performance of innovation processes by utilizing asymmetric input and output data. Therefore, this paper develops an improved SBM model analysis framework for evaluating the green innovation efficiency of asymmetric input and output data. The framework is applied to assess the technical (TE), managerial (PTE), and scale (SE) efficiencies of new energy companies under three input variables (R&D personnel input, R&D capital input, and comprehensive energy consumption input), two desirable output variables (green technology output and economic output), and one undesirable output variable (greenhouse gas emissions). Then, environmental factors and random factors are eliminated from the obtained input slack variables based on the SFA model, placing decision-making units in a homogeneous environment. The results demonstrate that TE, PTE, and SE are improved after eliminating environmental factors and random factors. Subsequently, based on the entropy method, this paper classifies companies’ green innovation patterns into four categories and provides targeted solutions. The purpose of this paper is to provide an evaluation method for new energy companies to understand green innovation efficiency and assist decision makers in identifying the most optimal resource allocation approach. The proposed improved SBM model contributes to the literature and to industry practice by (1) providing a reliable evaluation of green innovation efficiency under asymmetric input and output data; (2) determining effective improvement actions based on a slack analysis of environmental variables and random variables that lead to improved process performance; and (3) making fuzzy innovation performance efficient to facilitate understanding and managing innovation resource allocation quality.