Deviation model is an important model for through-flow analysis in axial compressors. Theoretical analysis in classical deviation models is developed under the assumption of one-dimensional flow, which is controlled by the continuity equation. To consider three-dimensional characteristics in transonic flow, this study proposes an improved theoretical analysis method combining force analysis of the blade-to-blade flow with conventional analysis of the continuity equation. Influences of shock structures on transverse force, streamwise velocity and streamline curvature in the blade-to-blade flow are analyzed, and support the analytical modelling of density flow ratio between inlet and outlet conditions. Thus, a novel deviation model for transonic stages in axial compressors is proposed in this paper. The empirical coefficients are corrected based on the experimental data of a linear cascade, and the prediction accuracy is validated with the experimental data of a three-stage transonic compressor. The novel model provides accurate predictions for meridional flow fields at the design point and performance curves at design speed, and shows obvious improvements on classical models by Carter and Çetin.