Newly developed airliners have adopted supplemental cooling systems (SCS) to provide for non-cabin cooling requirements. In the present study, dynamic component models for compressor and phase change heat exchangers were developed with dynamic decoupling and explicit solution methods, and pressure zone separation and solution methods are developed based to obtain dynamic pressures as key values. A dynamic VCRU subsystem model is established, and the result under single-unit startup condition shows pressure deviations less than 0.16 %, with a simulation time ratio of 5.65 %, exhibiting good overall performance at both precision and speed. A dynamic SCS system model is developed, and the simulation of a 9000 s flight took 1973.3 s to complete. Result in the cruise phase shows the condensation and evaporation temperatures are in the ranges of 28.39–31.33 °C and −17.93 to −10.71 °C, respectively, meeting their respective designed ranges of 30 ± 5 °C and −15 ± 5 °C. These results reflects good consistency of the model with actual system characteristics. Control optimization is conducted based on the developed model to eliminate temperature fluctuation. The optimization reduced the maximum temperature deviation from 0.4004 K to 0.0019 K after system starting process, proving the feasibility of control method optimization based on the developed dynamic simulation model.