Liquid-based battery thermal management system (BTMS) is commonly applied to commercial electric vehicles (EVs). Current research on the liquid cooling structure of prismatic batteries is generally focused on microchannel cooling plates, while studies on the discrete tubes are limited. In this paper, a parallel liquid cooling structure based on heat-conducting plates and cooling tubes is proposed, with computational fluid dynamics used to investigate the cooling performance of the structure. Two different optimization schemes are then put forward, and the effects of the coolant inlet velocity and temperature on the thermal management performance of the optimized structures are explored. Compared with the previous series structures for the same battery module, the parallel structure can significantly reduce the pressure drop and the flow resistance loss. The gradient structures increasing the parallel round tube inner diameters were able to reduce the pressure drop, while the heat transfer was slightly enhanced. Changing the contact mode between the heat-conducting plates and the square cooling tubes could effectively improve the temperature uniformity of the battery module, particularly for structures with no contact between the lower region of the first plate and the cooling square tube. Based on the gradual increase in the inner diameter of the round tubes, the structure of breaking the contact between the lower region of the first plate and the cooling square tube was able to reduce the maximum temperature difference in the battery module within 3 °C by 41.12% and the pressure drop by 26.28% compared with the original structure.