It is important for China's green innovation productivity and sustainable development to study the effect of heterogeneous environmental regulation on microenterprise innovation activities. Based on the panel data of high-tech enterprises in China from 2012 to 2017, the article studies the incentive effect of heterogeneous environmental regulation on technological innovation and the mediation of innovation input and explores whether different types of environmental regulations have interactive effects on enterprise innovation. The results reveal that compared with the command-controlled environmental regulation, the incentive effect of market-incentive environmental regulation and voluntary environmental regulation on enterprise innovation is more significant, where the innovation input fully plays its role as a mediating effect. Further research finds that there is an interactive effect between command-controlled environmental regulation and other two regulatory tools, but no interactive effect between market-incentive environmental regulation and voluntary environmental regulation, which shows that the control-based regulatory tools and more flexible regulatory tools have a complementary effect on enterprise innovation. Through revealing the internal mechanism of environmental regulation on enterprise innovation, the article displays the process of technological innovation, and it also finds that flexible regulation tools and the combination of rigid and flexible tools are more conducive to encourage enterprises to carry out innovation activities.