When the cascaded H-bridge converter operates unbalanced under active thermal control, the clamping H-bridge module generates a large number of harmonics around twice the carrier frequency. Aiming at this problem, a harmonic performance optimization strategy under active thermal control of the cascaded H-bridge converter is proposed. The harmonic distortion of the converter output voltage with the clamped H-bridge module under thermal control is analyzed in-depth, and an unconventional PSPWM based on the carrier angles correction of the H-bridge module is designed to eliminate the sideband harmonics of the double carrier frequency. Experiments were carried out using a prototype of the cascaded H-bridge converter, and the test result is that after adopting the harmonic performance optimization control, the dominant harmonics around twice the carrier frequency were eliminated, and the temperature of the clamping H-bridge module was reduced by 0.9°C. The test results show that the novel harmonic performance optimization strategy under the active thermal control can effectively improve the output harmonic performance of the cascaded H-bridge converter system and realize the thermal equilibrium of the H-bridge modules.