Agrifood land plays a crucial role in indigenous communities. However, there is limited study on the overall sustainability and inter-ethnic comparison of agrifood lands across ethnic groups. To address these gaps, we developed a visual eco-efficiency framework of ecological footprint, biocapacity, and ecological benefit to evaluate the sustainability of agrifood land in these regions, as well as analyzed the sustainability of agrifood land and examined its explanatory factors across six ethnic groups in the Yunnan Province of China. The results showed that the ecological benefits of agrifood lands fluctuated in a low ecological deficit, and the eco-efficiency of different ethnic groups varied significantly, from 2010 to 2020. Moreover, redundancy analysis showed that cash crops, forestry, fishery, and livestock were major contributors to the eco-efficiency of agrifood lands in ethnic groups, rather than the commonly accepted staple foods. Another finding revealed that the contribution of urbanization rate to the eco-efficiency of agricultural food land had a rule of reversed U and was influenced by the annual average temperature and the ethnic population rate. Our study not only provided a visual framework for evaluating the sustainability of agrifood land in ethnic areas but also shed new light on its explanatory factors across different ethnic groups. The study served as a scientific foundation for the investigation, monitoring, and management of indigenous agriculture by governments and the agricultural sectors.