To address the deformation compatibility issue between the gear body and the teeth in the meshing stiffness calculation of multi-web helical gears, this study integrates the finite element method (FEM) and the energy method to develop a meshing stiffness calculation approach for multi-web helical gear transmission systems. According to the meshing characteristics of helical gears, the meshing stiffness of sliced gear segments is superposed with a phase offset, enabling accurate determination of the meshing stiffness and the load distribution factor of multi-web helical gears. Taking a symmetric three-web helical gear as the research object, the effects of the rim thickness ratio, side-web thickness ratio, middle-web thickness ratio, and side-web offset on the meshing stiffness and load distribution factor are investigated. The distribution characteristics of the total meshing stiffness and the single-tooth meshing stiffness under different parameter settings are also discussed. The results show that the combined FEM–energy method can effectively capture the meshing stiffness distribution of multi-web helical gears with different web configurations. Increasing the thickness ratios of the side web, middle web, and rim all enhances the meshing stiffness, whereas a concentrated web arrangement leads to a substantial reduction in meshing stiffness. A rational design of the structural parameters of multi-web gears can improve the stiffness distribution and effectively reduce the load distribution factor.