It is the theme of today to develop green economy and improve environmental efficiency (EE). As a comprehensive index to measure energy input, economic output and environmental development, environmental efficiency (EE) is of great significance for China to realize the sustainable development of economy and environment. China is in a critical period of industrial transformation and upgrading and ecological civilization construction, the effect of the collaborative agglomeration of manufacturing and productive services on environmental efficiency has drawn attention from policymakers. In this study, the stochastic frontier approach (SFA) with unpaid input is used to measure the environmental efficiency (EE) of 66 cities in eastern China during 2009–2018. Population structure is regarded as a mediator to investigate the impact of industrial collaborative agglomeration on environmental efficiency based on the spatial econometric model. The results show that industrial collaborative agglomeration has a positive impact on environmental efficiency, which can be moderated by population density, aging and quality at the same time, while the moderating effect of population urbanization is not significant. Therefore, it is necessary to optimize the coordinated governance system of regional ecological environment, accelerate the construction of industrial collaborative agglomeration, and promote the sustainable development of industry and ecology with the advantage of population structure in order to improve environmental efficiency (EE).