Green innovation has become the goal for promoting the transformation and upgrading heavy pollution industries in the context of high-quality development, and the key factor for the success of green innovation is increasing the green innovation efficiency of heavy pollution industries. To understand the current situation of China's industrial innovation and get out of the dilemma, we use non-expected Slacks-based model (SBM) to measure green innovation efficiency in Chinese industry, Lasso regression to screen the influencing factors of heavy pollution industries, tobit regression to study the influence degree and direction of different influencing factors on green innovation efficiency of heavy pollution industry. The results show that: (1) The green innovation efficiency of the 16 heavily polluting industries studied in this paper is generally low; (2) Coordination, green and openness all have a positive impact on the green innovation efficiency of the industry. (3) A certain degree of government scientific research support is conducive to improving the efficiency of industrial green innovation and exceeding the limit will have a restraining effect on enterprise innovation. According to the results, we put forward the corresponding policy implications.