A new solution for the control rod cusping problem in the three-dimensional pin-by-pin core calculation is proposed in this paper. The current advanced nodal code resolves this issue by estimating the one-dimensional axial flux distribution in a partially rodded node. However, direct application of this approach to the three-dimensional pin-by-pin calculation is impractical since the leakage effect in the radial direction is significant and the one-dimensional model for axial flux distribution is no longer valid. This issue has been neither addressed nor resolved yet. In this paper, a new approach that utilizes the inverse of the spectral index obtained in the assembly calculation is used to estimate the flux distribution inside the partially rodded mesh. The proposed model was implemented in the SCOPE2 code, which is a three-dimensional pin-by-pin nodal-transport code for pressurized water reactor core calculations, and a verification calculation was carried out to confirm the validity of the proposed method. From the calculation results, oscillation in the differential worth of control rods (i.e., the cusping effect) is damped, and the proposed model can almost reproduce that obtained by the reference calculation. The additional computation time for the proposed model is negligible. Consequently, the proposed control rod cusping model is an attractive method in three-dimensional pin-by-pin calculations.