As the primary solution to the issue of high passenger traffic in urban areas, rail transit has a significant impact on the structural form of cities and regional development. Additionally, it has varying degrees of a premium effect on land value around stations. Current research on the factors influencing the premium effect of rail transit station areas mainly focuses on the macro level of the station area circle, with more attention given to the premium caused by distance and functional differences. Most research objects are typically urban center lines or stations. However, this study focuses on the core area of the station and concentrates on the impact of the construction of integrated station–city facilities on the choice of pedestrian routes and the enhancement of pedestrian accessibility. It also explores whether this enhancement is associated with the premium benefits of ancillary commercial development. To achieve this goal, this paper integrates models from several related studies to conduct a comprehensive assessment. Firstly, it uses a spatial panel econometric model to improve the classical characteristic price method model. It then combines the ideas and models of the cost–benefit analysis method, taking the Odakyu Odawara Line of the Japanese suburban railroad as an example. This analysis explores the mechanism and factors influencing the rent premium of commercial facilities in the suburban rail station area and systematically assesses the combined station–city facilities. The study evaluates the social benefits (enhanced walkability) and economic value (premium value added from commercial facilities) of the combined station–city facilities systematically. The results of the study show that (1) the premium benefits of suburban railroad station area commercial facilities are significantly related to the type of station–city combination facilities, combination mode, and walking time and weakly related to the location factor. Additionally, (2) the results of the cost–benefit valuation analysis based on the Ebina Station verify that a reasonable design of station–city combination facilities can effectively enhance the proximity of commercial facilities to the station and improve the walking accessibility, thus promoting the premium benefits. The study demonstrates that a reasonable design of the combined station and city facilities can effectively enhance the proximity of commercial facilities to the station and improve pedestrian accessibility, promoting premium benefits, which can quickly feed the construction cost of the station and achieve positive revenue in the short term. Therefore, the results of the study provide a quantitative reference for the planning and design of suburban stations.