In this paper, a new numerical modeling method that combines a modified electromechanical model with a Teflon ablation model is proposed to simulate the working process of micro-pulsed plasma thruster (µPPT). The ablation mass accumulation during the discharge process and the non-Fourier effect during the ablation process are considered to improve simulation accuracy. Simulation results are in good agreement with experimental results. Furthermore, the influence of both the electrical and structural parts on the performance of µPPT was investigated by applying the combined model. It was proven that large capacitance of the capacitor and large gap-to-plate-width ratios can effectively improve the comprehensive performance of the thruster concluding the specific impulse, impulse bit, and efficiency. The results not only validate the theoretical model, but also guide the design and operation optimization of µPPT.