Substantial development is needed in the production of pollution-free vegetables to ensure the quality, safety, and competitiveness of vegetables in China. In contrast to customary vegetable production, pollution-free production uses organic fertilizers and biological pesticides instead of chemical fertilizers and chemical pesticides. This mode of production improves the safety of the vegetables and reduces environmental pollution, and the government is encouraging its use throughout China. Nevertheless, there is still considerable scope for research into efficient and sustainable vegetable production. Emergy evaluation is an effective tool in analyzing the efficiency and sustainability of an ecological system, which addresses the weakness of traditional energy analysis and expresses different forms of energy using a common physical basis, namely, solar emergy. It also has the advantage of taking into consideration aspects such as natural resources, labor, and ecosystem services that are generally left uncalculated by other evaluation methods. This paper evaluated the efficiency and sustainability of a pollution-free vegetable production system based on emergy analysis, and results were compared with those of a customary vegetable production system. At the same time, the renewability factor of each input item was introduced in this study to improve analysis of the types of energy input. The emergy input structure and energy-based indices such as emergy efficiency (UEV), renewability (ΦR), net emergy yield ratio (EYR), environmental loading rate (ELR), product safety index based-emergy (PSI), emergy sustainability index (ESI), and emergy-based monetary value (EmRMB) were analyzed to estimate the efficiency and sustainability of the pollution-free vegetable system, and to determine the key points affecting the ecological performance of the system. The results showed that the total energy input of the two modes of the pollution-free vegetables production system were 4.97×10¹⁶ sej/year and 4.12×10¹⁶ sej/year, respectively. Compared with the customary vegetable production system, the UEV, EYR, ΦR, EPSI, and ESI values of the pollution-free vegetable production system rose on average by 24.3%, 24.9%, 36.0%, 98.2%, and 387.0%, respectively; and on average the ELR value declined by 64.7% and the EmRMB by 20.0%. At the same time, we found that that labor input and irrigation were the core factors that affected the efficiency and sustainability of the system. The scenario analysis revealed that the emergy efficiency and sustainability of the current pollution-free vegetable production system could be improved by 3.4%-10.8% and by 1.2%-31.7%, respectively, by creating an efficient system capable of adjusting to changes such as collection of rainfall to irrigate vegetables in a greenhouse, usage of electricity from a biogas project to irrigate, and reducing the labor input by applying standardized management. From an economic point of view, the reduction in purchased inputs and the higher price of pollution-free vegetables can be beneficial to the farmer. Moreover, the study demonstrates that the introduction of pollution-free vegetable production into recycling agriculture and the usage of biogas slurry as the main fertilizer have positive economic and ecological effects. Consequently, there is a considerable prospect for the development of pollution-free vegetables in China. The results also indicated that emergy evaluation is an effective method to analyze the vegetable ecological system and could provide a useful tool in the development of pollution-free vegetable production in China.