The biogas produced by the waste fruit and vegetable pile retting during the cold storage process is utilized. Subsequent to the decompression and purification treatment, a temperature control strategy is implemented in the enhanced cold storage area through the side load cooling cycle. The subsequent results demonstrate that the implementation of a biological natural gas cooling cycle, in conjunction with the criss-cross placement of shelves and a cargo frame tilt angle of 15°, as compared to shelf flat loading, results in a gradient distribution of regional temperature differences. This approach has been demonstrated to enhance the temperature uniformity index by 26.19%, increase the cooling rate by 3.36%, and reduce energy consumption by approximately 10.05%. Furthermore, the variation amplitude of the temperature non-uniformity coefficient of the shelf section is relatively gentle, with an average deviation of approximately 5.53%. The efficacy of this system in regulating temperature in time-sharing zones has been demonstrated. This system has been developed to facilitate the optimization of cold capacity, thereby ensuring the appropriate matching of cold storage capacity to the diverse needs of fruit and vegetable storage in different temperature zones.