Abstract: Uncertainty of reactor physical design is one of the necessary parameters for the QMU (quantification of margins and uncertainties) validation of the Generation-Ⅳ nuclear reactors, and uncertainty of nuclear data is an important source. Using BUND (burnup uncertainty of nuclear data) code to couple TRITON and TSUNAMI-3D modules of SCALE code, calculations of uncertainties for the effective multiplication factor k_eff in the molten salt reactor for Th-U and U-Pu fuel cycles were performed. The results were compared with the calculation results of uncertainty for k_eff by the covariance data from ENDF/B-Ⅶ.1. It is found that, at the beginning of life, the uncertainties for k_eff of Th-U and U-Pu fuel cycles are 0.490% and 0.582%, respectively, and they increase with burnup time. At the end of life, reaction channels ²³⁹Pu (nubar), (n，f), (n，γ), ¹⁰⁵Rh (n，γ), ¹³⁵Xe(n，γ) and ²³⁴U (n，γ), ¹⁴³Nd (n，γ), ^131,135Xe(n, γ) are significant for k_eff uncertainties of U-Pu and Th-U fuel cycles.