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An advanced nuclear reactor Generation IV, called MSR, has been developed with Thorium utilization for a sustainable energy system. In this paper, the reactor is designed with power operation of 250 MWt/100 MWe in five years without refueling. Fuel salt in the reactor is composed of a eutectic FLiBe, Thorium, and Plutonium, as a coolant, fertile, and fissile nuclide, respectively. Plutonium loaded is a weapon-grade which consist of 238Pu, 239Pu, 240Pu, 241Pu, 242Pu, and 241Am. Graphite is used as moderator; therefore, the reactor is operated in thermal energy range. The reactor design is calculated in neutronic terms with program code CITATION in SRAC 2006 with JENDL 4.0 as nuclear data library. The result shows some neutronic parameter changes with increasing Plutonium loaded. The utilization of Plutonium, in this case, is described as a capability of MSR in burning a high-level waste of nuclear and radioactive isotopes. This system can be dedicated to future cleaning energy production in a nuclear reactor.