Abstract: On-line refueling and reprocessing are the two most significant features of molten salt reactor (MSR), which are beneficial to improve the burnup and fuel utilization efficiency. The SCALE code is a comprehensive modeling and simulation suite for criticality safety, reactor physics, radiation shielding, radioactive source term characterization, and sensitivity and uncertainty analyses. However, it cannot be directly applied to simulate the burnup of MSR. Therefore, a special multi-fluid MSR refueling and reprocessing system analysis code (MSR-RRS) was developed by coupling the problem-dependent cross section processing module, the criticality calculation module and the burnup and decay calculation module in SCALE. MSR-RRS was used to simulate the behaviors of on-line refueling, on-line reprocessing and/or offline reprocessing fission products in MSR. Moreover, MSR-RRS was verified based on the single-fluid molten salt breeder reactor (MSBR) and two-fluid molten salt fast reactor (MSFR). The results indicate that MSR-RRS has a high accuracy with the benchmarks. In conclusion, MSR-RRS is suitable for various types of MSR and fuel cycles.