Abstract: To investigate the shear force distribution in composite single-box multi-cell girders with corrugated steel webs (CSWs), a novel high-order beam element (CSW-ESD) incorporating an equivalent shear deformation degree of freedom (DOF) was developed. By introducing shear stress distribution coefficients for top and bottom flanges, a quantitative relationship between the shear forces in concrete flanges and the equivalent shear strains of CSWs under bending was established, enabling effective separation of shear force contributions between concrete flanges and CSWs. Furthermore, the equilibrium equations of the micro-segment for both prismatic and non-prismatic composite box girders were unified. The influence mechanism of non-prismatic effects on shear force distribution was clarified, and the expressions for shear force distribution among different components under additional bending effects were refined, leading to the establishment of a theoretical model for shear force distribution in composite box girders with CSWs. Based on the finite element formulation, a CSW-ESD beam element was developed by adopting vertical displacement, equivalent shear strain, and equivalent bending rotation as nodal DOFs. The influence of diaphragms was incorporated through generalized displacement modes derived from the homogeneous solutions of the governing differential equations. Numerical results demonstrate that the CSW-ESD element can accurately predict the shear force distribution in both prismatic and non-prismatic composite box girders with CSWs. For prismatic girders, the shear force ratios among different components remain relatively stable, except in the vicinity of concentrated loads and diaphragms. In contrast, for non-prismatic girders, the shear force distribution is significantly affected by the reverse shear contribution of the bottom flange and the additional bending moment induced by axial force. This may lead to notable increases or decreases in the shear force carried by CSWs, and even to a “shear force over-distribution” phenomenon, indicating that the conventional assumption that “shear force is mainly resisted by CSWs” is no longer applicable. Moreover, due to the non-uniform distribution of flexural shear flow, the shear force in interior webs is consistently higher than those in the side webs. Therefore, it is recommended that the shear force of interior webs predicted by the CSW-ESD beam element be adopted as a rational and conservative design reference value.