The optimization of an integrated coal gangue system of mining, dressing, and backfilling in deep underground mining is a multi-objective and complex decision-making process, and the factors such as spatial layout, node location, and transportation equipment need to be considered comprehensively. In order to realize the intellectualized location of the nodes for the logistics and transportation system of underground mining and dressing coal and gangue, this paper establishes the model of the logistics and transportation system of underground mining and dressing coal gangue, and analyzes the key factors of the intellectualized location for the logistics and transportation system of coal and gangue, and the objective function of the node transportation model is deduced. The PSO–QNMs algorithm is proposed for the solution of the objective function, which improves the accuracy and stability of the location selection and effectively avoids the shortcomings of the PSO algorithm with its poor local detailed search ability and the quasi-Newton algorithm with its sensitivity to the initial value. Comparison of the particle swarm and PSO–QNMs algorithm outputs for the specific conditions of the New Julong coal mine, as an example, shows that the PSO–QNMs algorithm reduces the complexity of the calculation, increases the calculation efficiency by eight times, saves 42.8% of the cost value, and improves the efficiency of the node selection of mining–dressing–backfilling systems in a complex underground mining environment. The results confirm that the method has high convergence speed and solution accuracy, and provides a fundamental basis for optimizing the underground coal mine logistics system. Based on the research results, a node siting system for an integrated underground mining, dressing, and backfilling system in coal mines (referred to as MSBPS) was developed.