Based on the concept of comprehensive utilization of wastes, an eco-agricultural integrated production system of cattle, biogas, and greenhouse vegetables (IPSCBV) was constructed for a large-scale farm in Northwest China. In the present study, the production efficiency, environmental impact, economic viability, and sustainability of the IPSCBV were evaluated using emergy and economic analyses. The performance of the IPSCBV was compared with that of independent production systems for cattle and greenhouse vegetables using a variety of emergy indices, including the joint indices (transformity, emergy yield ratio, environmental loading ratio, and emergy sustainable index) calculated for the IPSCBV with multiple outputs and the weighted average indices for the independent production systems. The self-organization ability, emergy exchange status, and economic and environmental benefits of the integrated and independent production systems were evaluated using the feedback ratio of yield (FYR), emergy exchange ratio (EER), and greenhouse gases emission mitigation intensity (GEMI). The evaluation results using the new emergy-based indices showed that the IPSCBV had better emergy efficiency and higher sustainability, which resulted in less environmental stress than the independent production systems for cattle and greenhouse vegetables. The FYR of the IPSCBV system was 10.50% while that of the independent systems was only 0%. The GEMI in the IPSCBV reached 2.12kgCO2-eq/1014sej. The EER of the IPSCBV (0.62) was significantly lower than that of the independent greenhouse vegetable production system (3.02). That is, the price of the products underestimated their real (emergy-based) value which includes the free environmental resources and the system's inherent feedbacks. From an economic point of view, the IPSCBV may not provide a competitive economic input–output ratio in the short run. However, it serves as a promising eco-agricultural model for comprehensive utilization of wastes on large-scale farms associated with intensive management because of its better performance with respect to resource utilization, environmental emission mitigation, and sustainability.