STEP Cube Lab. classified as a pico-satellite has been being developed by SSTL(Space Technology Synthesis Laboratory) in Chosun University. Its main mission objective is to perform the on-orbit verification of core space technologies, which will be the potential candidates for future space missions. In this paper, to guarantee successful mission operation of the cube satellite under extremely severe space thermal environment condition, the system level thermal design and analysis has been performed. The effectiveness of the design has been verified through on-orbit thermal analysis of cube satellite.