There were two collection, transportation and treatment models for rural domestic waste management: urban–rural disposal model and area-based disposal model. In the urban–rural disposal model, rural domestic waste is collected in villages, transferred in towns, and disposed in centralized disposal sites of county, whereas area-based disposal model meant that each village built its own small-scale domestic waste facility. The threshold of transportation distance between urban centralized disposal sites and villages determined which of these two models would be more cost-effective. In this study, a distance decision-making model to obtain the threshold of collection and transportation distance was proposed. Besides, by application of this distance decision-making model supported by GIS software, 14588 villages of Guangxi Province, China were recommended to apply urban–rural disposal model or area-based disposal model. Results showed that (1) distance threshold decreases as the population of village increases; (2) when the population size of the village was up to 20000 people, it was more cost-effective choosing area-based disposal model; (3) a total of 10932 villages in Guangxi Province were recommended to select urban–rural disposal model, 71% of which should expand treatment scales of urban centralized disposal sites. In addition, 3554 villages were recommended to select area-based disposal model; (4) the parameters of amount of per capita domestic waste output, the average life of the facilities, cost of building new small-scale area-based treatment facilities, and cost of collection and transportation of waste have high sensitivity for distance threshold estimation.