Patent-intensive industries can promote high-quality development of economy; however, they also generate the environmental pollution. Therefore, it is necessary to evaluate their green innovation efficiency (GIE), and it is beneficial to improve the GIE of pantent-intensive industries. We treat the patent-intensive industries as the research objects, in which the new equipment manufactruing is more representative. Based on the projection pursuit model and the stochastic frontier model, we measure the GIE of the new equipment manufacturing and explore the factors affecting GIE. Also, we analyze the dynamic evolution trend of GIE of the new equipment manufacturing based on the dynamic evaluation model with speed characteristics. The research results demonstrate that there is still space for improvement in GIE of the new equipment manufacturing to a certain extent. The GIE of different new equipment manufacturing has obvious differences, and the development is uneven. R&D investment intensity and industry market competition have a positive effect on GIE, while government R&D support and external R&D expenditures have negative influence on GIE. The dynamic GIE of the new equipment manufacturing shows the fluctuating trend over time. The research conclusions provide implications for patent-intensive industries to increase GIE and achieve sustainable development.