This paper designs a dynamic management system for thermal energy in multi-temperature cold chains, constructs a monitoring system that includes sensor selection and lay-out, data acquisition and transmission, proposes a control strategy, and builds an intelligent platform. Through experimental simulation, in terms of temperature stability,co-ordinated control uses a coupling coefficient matrix to pre-compensate for adjacent zone interference, while paraffin’s stable phase change (205 kJ/kg latent heat) maintains temperatures during fluctuations. This synergy achieves 28.3% savings and 1.1 ℃ max deviation. In terms of energy saving effect, the energy saving rate of the entire temperature zone combination reaches 28.3%, and the energy consumption per unit time in the door opening stage decreases by 33.3%. The heat storage performance test reveals that the efficiency of paraffin decreases by 3.2% after 50 cycles, with a constant temperature time of 6.2 hours for heat release. The study shows that the system can effectively improve temperature stability and reduce energy consumption.