Biogas production is widely recognized as an effective solution for addressing agricultural waste treatment in rural areas. However, its development is often hindered by economic and environmental constraints. This study combined emergy evaluation and carbon footprint analysis methods to establish a new environmental radius assessment model for evaluating the ecological performance and optimization direction of an agricultural waste biogas production system, using a biogas production company in China as a case study. Compared with the straw return model and straw power generation model, the results of emergy indicators and carbon accounting showed that the biogas production model had a lower environmental load and higher economic output and level of emergy sustainability. Additionally, the biogas production system was found to reduce 0.47 kg of carbon emissions per 1 kg of agricultural waste utilized. The application of the biogas production model in rural areas had high ecological sustainability and carbon emission reduction benefits. Environmental radius assessment results confirmed that the reasonable changes in resource collection distance could further enhance the ecological sustainability, carbon mitigation ability, and economic benefits of the biogas production system. The environmental radius assessment method offers a new approach to the location planning of agricultural waste biogas utilization companies in rural areas.