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Sabu Raijua is one of the small areas in the East Nusa Tenggara (NTT) region with an electrification ratio that has not reached 100%. Additionally, the East Nusa Tenggara (NTT) region also faces a clean water crisis. High-Temperature Gas Reactor (HTGR) is a type of reactor that produces not only electricity but also could be used for cogeneration applications, such as desalination of seawater. In this research, the evaluation of the energy and seawater desalination process using HTGR was analyzed using the Desalination Economic Evaluation Program (DEEP) code. Meanwhile, calculation of reactor design performed by Standard Thermal Reactor Analysis Code (SRAC) code and using Japanese Evaluated Nuclear Data Library (JENDL) 4.0 as nuclear data library. The reactor was designed to produced 150 MWt power while seawater desalination used Multi-Effect Desalination (MED) method. As a result, this reactor design can meet electricity demand in the Sabu Raijua region. Also, seawater desalination yields 110000 cubic meters per day which are meet the needs of clean water.