Alternating magnetic fields can deliver magnetic energy deeper inside the body for magnetic hyperthermia cancer therapy by using magnetic nanoparticles (MNPs). In this study, we proposed a highly effective heat generation method for the MNPs by the application of an ultra-short pulse wave. We numerically evaluated the heating power with a variety of parameters, such as pulse width, field amplitude, and frequency. The hysteresis curve and magnetization dynamics clearly indicate larger energy dissipation. Hysteresis loss and the input energy increase with increasing field strength and duty ratio and there is a large efficiency power condition. To evaluate the effective heat generation and practical temperature increment, a larger imaginary part of magnetic susceptibility (χ″ > 30) and specific loss power (SLP > 105 W/kg) are required. In addition, larger intrinsic loss power (100 nHm2/kg) is achieved. The results indicate that the contribution of magnetic harmonics signals on the ultra-short pulse wave significantly enhances the heat generation of MNPs for cancer therapy.