At present, the field of cold chain logistics experiences significant growth, with refrigerator playing a pivotal role in cold chain transportation. An innovative compartmentalized phase-change cold storage refrigerator has been proposed in this study, designed to address the increasing demand for efficient and energy-saving solutions in the cold chain transportation industry. A conceptual module prototype is designed and built in this study, with an analysis of the system's charging and discharging processes under varying conditions. The cold storage refrigerator exhibits favorable matching characteristics, the charging process requires approximately 270 min, and the cooling effect sustains for about 23 h. A three-dimensional simulation model of the cold storage refrigerator is developed, enabling a comprehensive evaluation of the cooling effect and further optimization of the cold storage plate layout. The results indicate that the layout of the three-sided type cold plate significantly reduces the pre-cooling time. It is determined through simulation calculations in this study that setting the loading capacity to 50 % can strike a balance between efficient cooling and transportation efficiency. Additionally, under high-temperature conditions, the cold storage refrigerator maintains a low temperature for up to 10 h at a filling rate of 50 %.