The effect of flow direction on heat transfer in water cooling channel of lithium-ion battery is numerically investigated. Battery Design StudioⓇ software is used for modeling electro-chemical heat generation in the battery and the conjugated heat transfer is analyzed with the commercial package STAR-CCM+. The result shows that the maximum temperature and temperature difference of battery with Type 1 are the lowest because the heat transfer in the entrance region near the electrode is enhanced. As the inlet velocity is increased, the maximum temperature and temperature difference of battery decreases but the pressure loss increases. The pressure loss in Type 2 channel is the lowest due to the shortest channel length, while the pressure loss with Type 3 or 4 channel is the highest because of the longest channel length. Considering heat transfer performance and pressure loss, Type 1 is the best cooling channel.