The concept of “more- and all-electric aircraft” has become increasingly popular over the last two decades, leading to a boost in the extensive utilization of airborne electromagnetic actuators such as permanent magnet synchronous machines (PMSMs). Inevitably, considerable waste heat is generated during operation due to the incomplete energy conversion, which is a great challenge for conventional onboard thermal control systems. If the huge generated heat cannot be removed efficiently there will be a sharp temperature rise in thermal-sensitive components of the onboard devices. This overheating will cause operational failures which are intolerable in aerospace applications. Aiming to improve the current thermal protection system and gain greater compatibility with the current PMSM system, this paper proposes a phase change material-based (PCM-based) thermal protection strategy using commercial wax in two equivalent PMSMs. A comparative investigation shows that the machine temperature with PCM-based cooling strategy can be reduced under most operating conditions (the maximum temperature drop is 13.7 °C), demonstrating the advantages of deploying the proposed PCM-based cooling scheme. Further data processing towards the heat absorption-dissipation matching between the utilized PCM and the working mode of the cooling object is conducted. A dimensionless correlation of dimensionless temperature peak difference (DTPD) as a function of the pulsed factor, presented in Eq. (17), reveals an average relative error of ±4.5%. Based on the correlation, an optimal pulsed factor of ∼1.764 is calculated to reach a matching condition. Such a method can be promoted to wider applications using PCM as a cooling medium beyond the currently-utilized two types of machines in this paper.