As a new type of circulation corpus, the e-commerce of vertical fresh agro-products has been attached great expectations, and its efficiency will help to crack the circulation dilemma of fresh agro-products in China. This paper uses the three-stage DEA method to measure the efficiency of the e-commerce of vertical fresh agro-products based on the control of environmental factors and random errors. The major findings show that the efficiency is generally low, not only in scale efficiency, but also in management efficiency; environmental factors have a significant impact on the efficiency, of which the logistics’ infrastructure and population quality have a significant positive impact on the efficiency, while the level of informatization and regional economic development characterized by per-capita income have significant negative impact. The conclusions of this paper provide revelations for improving the e-commerce efficiency of fresh agro-products.