Abstract: With the increasing demand for high-performance microcryocoolers for use in high-operating temperature (HOT) infrared detectors, the electromagnetic stability of linear motors, which are the core driving components of linear Stirling cryocoolers, has become critical to the overall power consumption and performance consistency. In mass production, supporting structures such as coil holders, end caps, and mover frames may exhibit unexpected magnetic permeability owing to material impurities or manufacturing defects, leading to electromagnetic disturbances. This study systematically investigated the influence of such magnetic permeability disturbances in these supporting structures on the magnetic circuit distribution, electromagnetic spring stiffness, specific thrust, and overall cryocooler performance. An axisymmetric electromagnetic field model of a moving magnet linear motor was established using Ansoft Maxwell software. Simulation results revealed that permeable supporting structures cause magnetic flux line distortion, a static equilibrium point shift, and an asymmetric electromagnetic force. Experimental prototypes with non-magnetic (μ_r < 1.05) and magnetic (μ_r ≈ 1.20–1.25) supporting structures were fabricated. The electromagnetic spring stiffness, specific thrust, no-load current, end-stop collision power, and temperature-controlled power consumption were tested. The results showed that the presence of magnetic permeability in the supporting structures shifted the static equilibrium point toward the end cap side by up to 0.75 mm, increased the electromagnetic spring stiffness by more than 20%, and introduced significant asymmetry in the specific thrust (a maximum deviation of 2.56 N/A). Consequently, the resonance frequency drifted, the end-stop collision power decreased from 17.02 to 9.51 W ac on average, and the temperature control power consumption increased with degraded consistency (the standard deviation decreased from 0.31 to 0.13 W dc). The cryocooler with nonmagnetic supporting structures achieved a maximum cooling capacity of 2.3 W at 150 K under operating conditions of 120 Hz and 32 bar, with a Carnot efficiency of 11.2%, demonstrating excellent refrigeration performance. The results of this study provide theoretical guidance and a practical process-control strategy for designing high-consistency, low-power microcryocoolers.