In this paper, the reliability of super-junction MOSFET under single-pulse Unclamped Inductive Switching (UIS) was simulated using Sentaurus TCAD software. Through simulation of etching source metal, it was proved that the conduction of parasitic bipolar transistor in parallel multi-cell structure is the main cause of temperature concentration leading to burnout. The method of reinforcing super-junction MOSFET is proposed by using the conduction of parasitic transistors as the criterion for evaluating UIS performance. In the proposed two-layer alternating PN column stack structure, the upper PN columns have a charge imbalance structure with a higher p-column concentration than the n-column. The simulation results show that the improved structure has higher avalanche energy and wider process variation range compared to the traditional structure. Compared with the traditional device, the improved device achieves a continuous avalanche duration of 1.3 × 10−3 s and an avalanche robustness of 8.24 joules (J) when the parasitic bipolar transistor is non-conductive, significantly reducing the process difficulty by increasing the P-base concentration deviation to 5.8 × 1017 cm−3 under the same avalanche duration range.