Abstract: Thorium-based molten salt reactor (TMSR) is one of the fourth generation nuclear fission reactors. It uses FLIBE as the coolant, is capable of operating at high temperatures and has a high thermal efficiency. As the core of TMSR is composed of fuel pebbles and has a complex structure, three-dimensional model should be used. The research of using a three-dimensional model of RELAP5-3D method to replace the traditional one-dimensional system analysis is necessary. The applicability of RELAP5-3D in TMSR thermal-hydraulic simulation was analyzed by comparing the heat transfer model and pressure drop model of RELAP5-3D with the ones compatible for TMSR. The differences of the laminar flow, turbulence, convection transition empirical correlations and pressure drop empirical correlations were analyzed in order to verify the applicability of RELAP5-3D. According to RELAP5-3D three-dimensional modeling features, the three dimensional core model of TMSR was set up and steady-state calculation was executed and achieved. Under the same conditions, the results of core axial temperature were compared between RELAP5-3D and CFX, which further verify that the three dimensional modeling capability of RELAP5-3D is feasibility for TMSR. The TMSR core model was modified as a full loop model with pipes, pump and heat exchanger added. The steady-state calculation and LOFC accident simulation were executed and achieved. In general, according to the preliminary analysis and calculation, RELAP5-3D is basically feasible for TMSR thermal-hydraulic simulation and capable of preliminary thermal-hydraulic system analysis.