Focusing on the peculiarities of urban construction resulting from specific mountain terrains, the purpose of this study is to find out a suitable method based on a Spatial Network Comprehensive Model (SNCM) to reasonably plan and distribute primary schools in low-income mountain cities. The construction principles and advantages of the SNCM method are proposed and the method tested in Wanyuan city of Qinba Mountain area (Southwest China) to verify its feasibility and optimization. Taking account of the mountain terrain and its influence on user behavior, we used the SNCM method to build a comprehensive model which integrates the road slope and the walking speed of pupils into the basic spatial model. The model is used to calculate a reasonable layout of the primary schools and to validate the rationale. The results show that the SNCM method can be effectively applied in low-income mountainous cities. It can not only improve the accessibility and service efficiency of primary schools using as little capital-investment as possible, but also help the city grow in an intensive and efficient way.