Yield stress, as the key parameter to characterize the network strength of waxy oil, is important to the petroleum pipeline safety. Reducing the yield stress of waxy oil is of great significance for flow assurance. In this study, the effect of alternating magnetic field (intensity, frequency) on the yield stress of a waxy model oil with nanocomposite pour point depressant (NPPD) is systematically investigated. An optimum magnetic field intensity and frequency is found for the reduction in yield stress. When adding with NPPD, the heterogeneous nucleation of NPPD contributes to the reduction in yield stress for waxy model oil. Interestingly, the magnetic field is helpful for the modification of yield stress at a lower frequency and intensity before the optimal value; however, the modification is found to be weakened when the magnetic field is further increased after the optimal value. Possible explanation is proposed that the aggregation morphology of wax crystal would be altered and results in the release of wrapped oil phase from the network structure under the magnetic field.