There are obvious differences between different types of environmental regulation, which are manifested in different environmental protection tendencies and goals, and there are also significant differences in policy implementation. Therefore, it is an urgent empirical problem to quantitatively evaluate the impact of heterogeneous environmental regulation on the upgrading of industrial structures. Therefore, on the basis of measuring the level of industrial structure upgrading, this paper empirically tests the impact of heterogeneous environmental regulation on industrial structure upgrading. The results show that the upgrading level of China's industrial structure increased year by year from 2000 to 2018. The three types of environmental regulatory measures have effectively promoted the upgrading of the industrial structure, and the market-incentive environmental regulation (MER) has a significantly higher role in the advancement of the industrial structure than the command-controlled environmental regulation (CER) and the voluntary public participation environmental regulation (VER). With the improvement of regional economic development level, the three types of environmental regulation have gradually become more prominent in promoting the upgrading of industrial structure. In the mechanism test, it is found that technological innovation has a partial mediating effect in the process of CER affecting the upgrading of industrial structure, MER and public VER have a complete mediating effect, while foreign direct investment (FDI) has only a partial mediating effect in the process of the three types of environmental regulation affecting industrial advancement, and there is no mediating effect in the process of influencing the rationalization of industrial structure.