Abstract: Thermal-hydraulic simulation analysis is an important part of reactor system design and safety analysis. The system program represented by RELAP5 can quickly analyze transient or accident conditions. Meanwhile, the computational fluid dynamics (CFD) code represented by FLUENT analyzing local 3D phenomena is also increasingly important. In order to make full use of the advantages of both, a RELAP5/FLUENT coupled program was developed by the secondary development of the RELAP5 source code and FLUENT UDF. The coupled program was verified by using the problem of flibe molten salt flowing in a horizontal pipe. A steady-state simulation was performed for the 2 MW molten salt reactor, and the coupled program can analyze the physical phenomenon of the molten salt reactor core in detail. Finally, the transient thermal-hydraulic behavior of a 2 MW molten salt reactor with an abrupt power was simulated. Compared with the RELAP5, the coupled program can better reveal the physical phenomenon of the molten salt reactor core. This coupled program can be used to solve the problem of some significant three-dimensional mixing phenomenon in the thermal-hydraulic analysis of molten salt reactor.