Molten salt reactor (MSR) is one of the non-pressurized-water fourth-generation reactors that uses liquid nuclear fuel that integrates coolant and nuclear fuel, so it is a safe reactor that can fundamentally prevent severe accidents caused by coolant loss. MSR uses NaCl-MgCl2 as a coolant salt, which is considered a promising diluent that can dissolve the fuel salt by forming an eutectic mixture. In this study, a zone-melting system was used to remove impurities from the NaCl-MgCl2 used in MSR. The system was designed in detail to control eutectic salt impurities by traversing long charges into a small molten zone.