The objectives of this paper are: (1) to conduct the thermal analyses of the disposal cell using COMSOL Multiphysics; (2) to determine whether the design of the disposal cell satisfies the thermal design requirement; and (3) to evaluate the effect of design modifications on the temperature of the disposal cell. Specifically, the analysis incorporated a heterogeneous model of 236 fuel rod heat sources of spent nuclear fuel (SNF) to improve the reality of the modeling. In the reference case, the design, featuring 8 m between deposition holes and 30 m between deposition tunnels for 40 years of the SNF cooling time, did not meet the design requirement. For the first modified case, the designs with 9 m and 10 m between the deposition holes for the cooling time of 40 years and five spacings for 50 and 60 years were found to meet the requirement. For the second modified case, the designs with 35 m and 40 m between the deposition tunnels for 40 years, 25 m to 40 m for 50 years and five spacings for 60 years also met the requirement. This study contributes to the advancement of the thermal analysis technique of a disposal cell.