As the backbone of the national innovation system, enterprises are the key drivers of economic development and environmental sustainability. However, at the microlevel, research in this area is lacking, as attention is paid on the comprehensive capabilities of top managers, industrial heterogeneity, and heterogeneous green innovation (GI), including inventive innovation and utility innovation. Based on Upper Echelons Theory, this paper constructs a research framework to explore and empirically analyze the specific impact of managerial capacity (MA) of top managers, as “gatekeepers” of enterprise decision‐making, on the heterogeneous enterprise GI, as well as its potential mechanism. Our results shows that (1), overall, MA can significantly promote GI of enterprises. Interestingly, compared with green strategic innovation, managerial capacity has a greater effect on green inventive innovation; (2) based on industrial heterogeneity, in heavy‐polluting industries, managerial capacity is more likely to promote green strategic innovation rather than green inventive innovation; (3) further analysis shows that enterprise value, internal control quality, and financing constraints are important mechanisms; and (4) the moderating effect of external environment shows that to some extent either the regional marketization level or management capabilities can drive GI. This paper has practical implications for policymakers and corporate managers adopting the management heterogeneity perspective and suggests areas for future studies in this field to promote green low‐carbon transition.