To solve the problem of low heat dissipation efficiency for the conventional S-type runner water-cooling plate of the fan converter IGBT module, two new water-cooling plates were designed with rectangular and elliptical column structures in the S-shaped runner of the water-cooling plate. The heat dissipation performance, the fluidity of cooling water, and pressure drop of different spoiler column structures were compared using Fluent software for the simulation and experiment. The comparative results show, compared with the water-cooling plate without a spoiler column in the flow channel of the control group, that the spoiler column structure in the flow channel significantly improved the heat dissipation performance of the water-cooling plate. When the inlet velocity of the water-cooling plate was 2 m/s, the highest temperature inside the water-cooling plate with a rectangular spoiler column structure was 12.25 °C, lower than the control water-cooling plate. The highest temperature inside the water-cooled plate with an elliptical structure was 12.40 °C, lower than the control water-cooled plate. The obstructive effect of the elliptical spoiler column structure on water flow was smaller than in the rectangular spoiler column structure. The fluidity of the cooling water inside the elliptical spoiler column structure water-cooling plate was better. When the inlet velocity of the water-cooling plate was 2 m/s, the cooling water flowing through the former was 282 L more than the latter in half an hour. Compared to the pressure drop, we found that in the design group, the pressure drop of the water-cooled plate with a rectangular spoiler column structure was 40,988.3 Pa. The pressure drop of the water-cooled plate with an elliptical spoiler column structure was 25,576.6 Pa. The difference between the two was 15,411.7 Pa, which proves that the energy loss inside the latter is smaller. To further explore the relationship between the heat dissipation and energy consumption of the two types of water-cooled plates, the comprehensive evaluation index η was calculated, ηb = 26.2, ηc = 31.6; therefore, ηb was significantly smaller than ηc. The overall performance of the water-cooled plate with an elliptical spoiler column structure was superior.