Plateaus, one of the most important terrain types in China, contain high-quality agricultural and livestock resources. However, due to their natural conditions, they host major deficiencies in cold chain logistics. Existing studies have focused on improving the temperature regulation capabilities of cold chain vehicle refrigeration or air conditioning systems, but have neglected the unique low-pressure environment faced by the Plateau cold chain transport vehicles. Using zoning design, air and vapor cycle refrigeration technologies, this study proposed a bootstrap-type integrated environmental control system (BIECS) and simple-type integrated environmental control system (SIECS) to realize vehicle “micro-environmental control.” The analytical solution of the thermal characteristics of the system was obtained based on the scaling-endoreversible thermodynamic analysis model. Moreover, the influence of ambient humidity on the thermal performance of the system was evaluated based on the enthalpy method. According to the typical working conditions, the system performances using different refrigerants, R404A, R448A, and R452A, were analyzed at different trailer temperatures, cooling capacities, and altitudes. Our results showed that, under the same design requirements, the coefficient of performance (COP) of the BIECS was slightly higher than that of the SIECS. Higher the trailer temperature and cooling capacity, higher is the COP of the system. Comparing the three refrigerants under the same working conditions, compared with R404A, the COP of the BIECS and SIECS increased by 13.4% and 10.9%, respectively, using R484A, and increased by 6.1% and 5.0%, respectively, using R452A. The performance of the systems that used R448A was the best. The system could ensure a 2.4-km cab pressure altitude at an ambient altitude of 5 km, but the COP could decrease by 31.8–35.6%, compared to that on the plains. This study provides and comprehensively evaluates a new technical solution for the environmental control of Plateau cold chain transportation vehicles. It also provides comprehensive health protection measures for drivers and technical support for the promotion and development of Plateau cold chains.