A research for transmutation reactor is in progress to transmute high radioactive isotopes into low radioactive ones. In this study, thermal-hydraulic and structural analysis was performed to design liquid metal target system that would be used in subcritical transmutation reactor. Diffuse plate installation was considered to enhance cooling of window. And thermal-structural analysis of window was performed varying window thickness, beam power, and coolant flow rate to determine target system design valuers. It is ensured that maximum window temperature and stress would be acceptable in the design condition.