From the standpoint of green patents, verifying the influence of the construction of national high-tech zones on the degree of green innovation of enterprises is of enormous theoretical and practical importance. We construct a multi-period two-difference model to assess the influence of the national high-tech zone policy’s implementation on enterprises’ levels of green innovation. The outcomes of the study show that: first, the establishment of national high-tech zones greatly increases the level of green innovation among enterprises. While the effect on green and practical patents is average, the effect on green invention patents is more obvious. Second, how enterprises in national high-tech zones promote green innovation varies significantly. Promotional effects are more prominent in Tier 1 and Tier 2 regions, non-state firms, and high-tech industries with significant economic development. State-owned enterprises, non-high-tech industries, and third-tier and lower-tier regions, on the other hand, fared brilliantly. Third, additional action mechanisms show that the establishment of national high-tech zones can contribute to the institutional environmental effects of enterprises and the concentration of green innovation elements, thereby realizing regional green innovation development. Thus, our research provides an empirical foundation for stimulating the formation of national high-tech zones, increasing firms’ ability to innovate on their own, and nurturing the long-term growth of national high-tech zones and associated businesses.