<p>Permanent magnet synchronous motors (PMSMs), due to their high efficiency, high power density, and rapid dynamic response, are extensively used in CNC machine tools, electric drive systems, and aerospace applications. However, traditional space vector pulse width modulation (SVPWM) techniques, which rely on fixed switching frequencies, often result in the accumulation of high-frequency harmonics. This accumulation can degrade electromagnetic compatibility and compromise the operational stability of the system. Aiming to address this issue, a stochastic SVPWM modulation strategy based on chaotic–Markov chain perturbation and coordinated parameter optimization is proposed to suppress high-frequency harmonic aggregation. This strategy establishes a dynamic and randomized SVPWM modulation framework by integrating Logistic–Tent chaotic mapping with a two-state Markov model. In addition, the GA–HIDMS–PSO algorithm is introduced to globally optimize the perturbation sequence parameters, transition probabilities, and frequency bandwidth. Simulation and experimental results confirm that the proposed method effectively suppresses harmonic peaks and broadens the spectral energy distribution in the high-frequency range, substantially outperforming the conventional RSF–SVPWM methods. The primary innovation of this study lies in the development of a modulation framework that combines a perturbation modeling mechanism with global optimization, specifically designed to control high-frequency harmonics in PMSMs. This study provides a novel and effective solution for harmonic suppression and ensures stable motor operation under complex working conditions.</p>