Abstract: Considering the continually rising tendency of the power densities of nano-satellite, MEMS (micro electro mechanical systems)based pumped liquid microchannel cooling system was introduced. Dynamical thermal response model for the temperature changes of both the controlled object and the cooling device was built up by means of the lumped parameter method with reasonable analysis and logical simplification. Based on the nanosatellite inorbit case, the variation rule of the internal electronic equipment and external radiator surfaces were performed by the numerical simulation and calculation. Simulation results indicate that MEMS based on the microchannel cooling system can satisfy the cooling requirements of nano satellite thermal system with high heat flux; the external space heat flux has less affect to the radiator of nano satellite compared with the internal equipment; the modeling methods and algorithm is convenient and reasonable not only for the dynamical temperature calculation and the analysis of nano satellite, but also for the developing of advanced nano-satellite thermal control and thermal management theories and technologies.