Battery thermal management (BTM) has an important significance for electronic vehicles to keep them operating in a reasonable temperature range and reduce local temperature differences. In this study, a novel structure of liquid cooling-based lithium-ion battery module with a variable contact area of heat-conductive blocks is proposed. Three-dimensional transient simulations are carried out to investigate the thermal performance of the proposed structure. The effects of block height, height gradient, and inlet velocity are discussed. The results indicate that simply increasing the height of heat-conductive blocks could have a negative effect on cooling performance and that a variable heat transfer area could efficiently improve the temperature uniformity of the battery module. In addition, the thermal performance of the proposed battery module is sensitive to inlet velocity, but the positive effect can be decreased when the velocity is adequately increased. The temperature difference (ΔT) of the battery module with a variable contact area can achieve below 4 °C, and its reduced percentage can be 47.7% compared with that of the module with a consistent contact area when the inlet velocity is 0.2 m/s.