Dynamic simulation model of air-cycle refrigeration systems in civil aircrafts is essential for revealing the operation mechanism during flight process. In the present study, a dynamic model of three-wheel air-cycle refrigeration system was developed. A near-logarithm heat transfer temperature difference function is utilized to improve the stability of the heat transfer solution. A dynamic solution method based on continuity equation and theorem of momentum was presented as the framework of the dynamic mass transfer solution. A pressure-flow decoupling method is presented to solve the dynamic pressure in the high-pressure zone, resolving the absence of key pressure parameters. The model has been validated based on experimental data, with a pack discharge temperature deviation of 0.05K. Dynamic simulations have been conducted with actual flight data to obtain transient performance under airborne condition. In the takeoff and landing phase, the drastic change in the environment results in low discharge temperature, endangering the condenser with icing risk, which can be avoided by enabling the TCV. In the cruise phase, the discharge temperature slightly exceeds the upper limit for a couple of minutes. The optimization by slightly extending the length of heat exchanger channels succeeded in eliminating the excessive discharge temperature with minimal side effects.