To make better use of agricultural residues and solve the problem of residues pollution, it is necessary to carry out regional management, which means spatial planning of the entire region is essential. This study developed a methodology based on GIS for determining the suitable locations, optimal sizes and number of biogas plants for the entire region while meeting the conditions that all biomass can be collected. Based on the optimization of transportation distance, the nearest facility model and the modified location allocation model were used to obtain the correspondence between plants and supply points, the transportation path and the plants’ capacity under different numbers of plants. Based on economic optimization, the economic model was constructed to calculate the total cost of different numbers of biogas plants and the optimal number was obtained after comparing. The cross path was adjusted for the selected plan to ensure that there was no crossover in the plants’ collection area. This approach was applied (as a case study) in Funan County, Anhui Province. Based on the existing results, the optimal construction number of biogas plants in the region was 9.