In this paper, the principle of spacecraft space heat flow simulation control system and its hardware and software structure are introduced. Then the algorithm and control mode of the software program used in the control system are analyzed simply. In the end, the optimization design of heat flow simulation software and its configuration file is expounded according to the complexity and diversity of control mode in vacuum thermal test, the different driving mode and communication interface of different program-controlled power supply. At present, the reliability of the optimized software has been verified in the thermal tests of the spacecraft components.