Industrial co-agglomeration is an advanced stage in the dynamic evolution of industrial agglomeration, which is crucial for promoting industrial transformation, promoting green development, and achieving economic growth. Based on panel data from 285 cities from 2004 to 2017, the spatial effects and regional heterogeneity of the co-agglomeration of manufacturing and productive service industries on green economic efficiency was empirically explored by using a spatial econometric model. The results show that the impact of industrial co-agglomeration on green economic efficiency show an inverted U-shaped pattern, with a promoting effect on its own green economic efficiency and a spillover effect on neighboring cities. Moreover, the spillover effect on neighboring areas is greater than that on the local green economic efficiency. In cities with higher administrative levels, the synergistic agglomeration of manufacturing and high-end productive service industries can promote the improvement of local green economic efficiency, but excessive agglomeration can also lead to economies of scale. Ordinary prefecture level cities should combine their own manufacturing development status, develop general productive service industries, and introduce high-end industries.