To investigate the effect of the location of vacuum insulation panels on the thermal insulation performance of marine reefer containers, a 20^ft mechanical refrigeration reefer container was employed in this paper, and the physical and mathematical models of three kinds of envelopes composed of vacuum insulation panels (VIP) and polyurethane foam (PU) were numerically established. The heat transfer of three types of envelopes under unsteady conditions was simulated. In order to be able to analyze theoretically, the Rasch transform is used to analyze the thermal inertia magnitude by calculating the thermal transfer response frequency and the thermal transfer response coefficient for each model, and the results are compared with the simulation results. The results implied that the insulation performance of VIP external insulation is the best. The delay times of each model obtained from the simulation results are 0.81 h, 1.45 h, 2.03 h, and 2.24 h, while the attenuation ratios are 8.93, 20.39, 20.62, and 21.78, respectively; the delay times calculated from the theoretical analysis are 0.78 h, 1.43 h, 1.99 h, and 2.20 h, respectively; and the attenuation ratios are 8.84, 20.31, 20.55, and 21.72, respectively. The carbon reduction effect of VIP external insulation is also the best. The most considerable carbon reduction is 3.65894 kg less than the traditional PU structure within 24 h. The research has a guiding significance for the research and progress of the new generation of energy-saving reefer containers and the insulation design of the envelope of refrigerated transportation equipment.