When new rail stations or lines are planned, long-term planning for decades to come is required. The short-term passenger flow prediction is no longer of practical significance, as it only takes a few factors that affect passenger flow into consideration. To overcome this problem, we propose several long-term factors affecting the passenger flow of rail transit in this paper. We also create a visual analysis of these factors using ArcGIS and construct a long-term passenger flow prediction model for rail transit based on a class neural network using an SPSS Modeler. After optimizing relevant parameters, the prediction accuracy reaches 94.6%. We compare the results with other models and find that the neural network model has a good performance in predicting long-term rail transit passenger flow. Finally, the factors affecting passenger flow are ranked in terms of importance. It is found that among these factors, bicycles available for connection have the biggest influence on the passenger flow of rail stations.