This paper addresses the optimized thermal modeling methodology for spacecraft board level thermal analysis. A direct thermal modeling of external and internal structure of active parts which have high power dissipation is newly proposed, based on conventional plate modeling for Printed Circuit Board(PCB). The parts thermal modeling results were compared with other generic methodologies and verified by thermal vacuum test. This parts thermal modeling was directly applied to thermal analysis of CS(Communication Subsystem) board of HAUSAT-2 small satellite. As a result, it was confirmed that the parts thermal modeling can complement other conventional modeling methodologies. A parts thermal modeling is very effective for thermal control design, since the existing thermal problems can be solved at the parts level in advance.