This study examined the impact of green finance policy on the green innovation efficiency (GIE) of the manufacturing industry in China based on data between 2005 and 2019 using a difference-in-difference model. The results indicate that implementing the green finance policy reduced the GIE of heavy-polluting industries compared with that of non-heavy-polluting industries. In terms of industry-specific heterogeneity, the green finance policy had a significant negative effect on the GIE of the textile industry, non-metallic mineral products industry, ferrous and non-ferrous metal smelting and rolling processing industry, chemical fiber manufacturing industry, metal product industry, leather and other related industries, and pharmaceutical manufacturing industry. However, it had a significant positive effect on the GIE of the chemical raw material and chemical product manufacturing industry, agricultural and sideline food processing industry, and papermaking and paper product industry. Furthermore, it also promotes the GIE of environment-friendly industries. In terms of factor heterogeneity, the green finance policy has had a positive effect on GIE improvement in technology- and capital-intensive industries. Moreover, it has inhibited GIE improvement in labor-intensive industries. To promote the GIE in manufacturing, a series of policy recommendations have been put forward.