Industrial enterprises are characterized by significant energy consumption and high emissions. Therefore, the implementation of green innovation by these enterprises is beneficial for promoting sustainable economic development and safeguarding the ecological environment. In this study, a relational two-stage DEA model containing shared inputs and undesired outputs is constructed to evaluate and decompose the green innovation efficiency (GIE) of Chinese industrial enterprises across 30 provinces from 2012 to 2021. Since the objective function of this model is nonlinear, a heuristic search method is employed for its resolution. On the basis of efficiency evaluation, the Gini coefficient, kernel density estimation, and convergence analysis are further employed to investigate the regional disparities and convergence properties in the two-stage efficiency of green innovation. Our findings are as follows: (1) The average GIE of Chinese industrial enterprises demonstrates a fluctuating upward trajectory, with significant regional disparities observed between provinces. (2) Regional disparities in R&D efficiency (RDE) and achievement conversion efficiency (ACE) have diminished in all regions. Super-variable density and interregional differences serve as the primary sources of regional disparities in RDE and ACE, respectively. (3) The presence of absolute and conditional convergence in RDE and ACE is observed across all regions. To improve the GIE of Chinese industrial enterprises, it is imperative to emphasize the heterogeneous impact of economic levels, industrial structure, and the degree of openness across various regions and stages of green innovation.