The optimal performance of a Li-ion battery is directly impacted by temperature. In order to control the temperature rise and provide even temperature distributions in the battery pack, a thermal management scheme comprises thin heat sinks with multiple phase change materials (PCMs) and air channels is investigated in this paper. The cooling performance and temperature homogenization of the battery thermal management (BTM) system are carefully studied under various configurations of PCMs. The results show that increasing the air inlet velocity has less effect in suppressing the temperature rise at early discharge stage, but ameliorates as the discharge prolonged to 3600 s. The standard deviation of the temperature (STDV) and maximum temperature of the batteries can be decreased by arranging PCMs with a lower melting temperature at the midsection and a higher melting temperature at the air outlet region of the heat sinks. In addition, for volume fraction of PCMs, Case IV, having a PCM with a higher melting point adjacent to the air outlet region and occupying one-half the height of the heat sink, illustrates a lower temperature rise and decreases the maximum temperature in the battery module by 1.024 K, 2.186 K, and 2.553 K, compared to Case I, II, and III, respectively.