Eco-efficiency enhancement is an inherent requirement of green development and an important indicator of high-quality development in general. It aims to achieve the coordinated development of nature, the economy, and society. Therefore, eco-efficiency measurements should focus on not only total factor input, but also process analysis. Based on the “full world” model in ecological economic theory, this study constructed a theoretical framework for a composite economic-environmental-social system that reflects human welfare and sustainability. To this end, using network data envelopment analysis (DEA), this study established a staged eco-efficiency evaluation model that uses economic, environmental, and social factors to measure the overall and staged eco-efficiency of China’s provinces from 2003 to 2016 and analyze its spatiotemporal characteristics. A geographically weighted regression (GWR) model was also used to analyze the influencing factors of eco-efficiency changes and the spatial differentiation in their effect intensity. The findings were as follows: (1) China’s overall eco-efficiency is still at a low level. It varies significantly from region to region, and only three regions are at the frontier of production. The eastern region has the highest eco-efficiency, followed by the central region, and the gap between the central and western regions has gradually narrowed. In terms of staged efficiency, the level of eco-efficiency in the production stage is less than in the environmental governance stage, which is less than that in the social input stage. (2) In terms of the efficiency of each stage, the efficiency level of the production stage showed a downward trend throughout the entire process, and the decline in the central and western regions was more obvious. The social input stage and the environmental governance stage both showed upward trends. The social input stage showed a higher level, and the increase was relatively flat during the period of study. Efficiency continued to rise during the environmental governance stage from 2003 to 2010 and rose overall, but with some fluctuations from 2011 to 2016. (3) Geographically weighted regression showed that the effects of the influencing factors on eco-efficiency had obvious spatial heterogeneity. The factors affecting overall, production stage, and social input eco-efficiency were, in order of effect intensity from high to low, economic growth level, marketization level, and social input level. In terms of environmental governance, social input level had the greatest impact, followed by economic growth; marketization level did not show a significant impact.