The design and numerical analysis of the two-layer PCM (Phase Change Material)-based thermal management system for a 18650-type lithium-ion battery have been performed. In relation to simulation, the coefficient of thermal conductivity and melting temperature of the first layer of PCMs are varied. Other parameters are made identical to that of the next layer's parameters in order that the generation of two different layers of PCMs can be attained: PCM-1 and PCM-2. To obtain a more realistic approach in the numerical analysis, the battery thermal model was created in the COMSOL-MATLAB interface using the experimental internal resistance data obtained for 18650 type Li-ion batteries in the literature. While a cheaper and more accessible material with a thermal conductivity of 0.2 W/mK and a melting point of 50 °C was used in the PCM-2 layer, the thermal conductivity was changed to 0.2; 1 and 5 W/mK in the PCM-1 layer; and the melting point was changed to 30, 40 and 50 °C. In this way, for PCM layers with different thickness (tpcm), the system was optimized at two different discharge rates, 5C and 7C. As a result of the numerical analysis, it was determined that the optimum tpcm, kpcm,1 and Tm values for the 5C discharge rate were 2 mm, 0.2 W/mK and 40 °C, respectively; and the optimum tpcm, kpcm,1 and Tm values for the 7C discharge rate were 4 mm, 5 W/mK and 40 °C, respectively.