In traditional train–bridge coupled system (TBCS), simply supported box girder bridges are often modeled using Euler beam elements, neglecting their spatial structure. This simplification may yield inaccurate results, impacting the running safety analysis of high-speed railway. To address this issue, a novel train–bridge interaction computational framework based on first-order shear deformation theory (FSDT) and radial point interpolation method (RPIM) for the box girder bridge model is proposed. In this model, the displacement fields of top, bottom, and web plates are represented using FSDT and numerically discretized by RPIM. The traditional TBCS is upgraded by replacing the Euler beam model with the novel model. This is the first time that the framework has been applied to TBCS field. Several numerical examples are presented to highlight the accuracy of this novel model, and illustrate the differences, and advantages of it over the traditional model. The results indicate that the proposed model closely matches the accuracy of the solid element (C3D20) model; it can provide a comprehensive bridge response compared to traditional TBCS, and the latter may underestimate the dynamic response of the structure. The proposed model holds significant potential for the simulation of box structures and widespread application in the field of TBCS. •A new meshless model is proposed for box girder bridge and other box structures.•This is the first time that the FSDT-RPIM computational scheme has been integrated into high-speed railway field.•The proposed novel model can provide new insights and detailed responses for the simulation of train–bridge coupled system.