To increase torque and power conversion of permanent magnet synchronous motors (PMSMs) at high-speed operation, the DC-link voltage of the inverter must be fully utilized during steady-state and transient operations. This paper proposes the incorporation of a harmonic reference generator (HRG) with a pulse clipping (PC) scheme into a model predictive control framework to achieve highest power output. The HRG calculates flux references in the stator-fixed coordinate system for an underlying continuous control set model predictive flux control (CCS-MPFC). These reference trajectories contain the harmonic flux component induced by the voltage hexagon in the overmodulation range and specific switching states (e.g., six-step operation) of the inverter are ensured by the proposed PC scheme. This enables a seamless transition to the overmodulation range including six-step operation and increases the drive’s power conversion to its maximum extent. Since the flux differential equation in the stator-fixed coordinate system, used as motor model for the HRG and CCS-MPFC, is able to represent PMSMs with linear and nonlinear magnetization, the proposed approach is well suited for the control of PMSMs with nonlinear magnetization. Extensive transient and steady-state experimental investigations on a highly utilized PMSM in the entire modulation and speed range prove the performance of the proposed approach.