For liquid cooling system special on the plane, because the change of the flight altitude the ram air temperature and flow rate of change, so that the system has some changes, at the beginning of the system design, the huge amount of computation and the complex working conditions, based on this, this paper uses Simulink simulation platform Matlab, to establish the dynamic mathematical model of main parts of liquid cooling system at on the basis of previous studies, and establishes the system simulation model and simulation analysis of system. Comparing the simulation results with the experimental data, verify the simulation analysis are in high accuracy, prove that the simulation system can play an important role in the design and optimization of the follow-up of the liquid cooling system.