Producing medical radionuclide 99Mo in molten salt reactors is a very attractive choice to solve its global shortage. In this study, we evaluated the yield of 99Mo in the small modular thorium based molten salt reactor (SM-MSR). Firstly, the fuel burn-up analysis of SM-MSR was carried out by an in-house developed code (MOBAT), which takes the unique characteristics of molten salt reactor into account, and the variation of fission yield of 99Mo with burn-up time was obtained. The minimum value of the fission yield of 99Mo is 1.13 × 10−3 (6-day TBq/MW/s) at approximately 600 equivalent full power day. Then, based on the behavior of noble metals in the fuel salt and the experimental results of MSRE gas sample composition measurements, 99Mo migration probability from the primary loop to the off-gas module with the burn-up time was calculated, and the equilibrium value of the migration probability is obtained as 18.4%. When the load factor of SM-MSR is 0.75 (300 MWth), the annual 99Mo amount of migration to the off-gas module would be 1.96 × 106 (6-day TBq) under the most conservative calculation. Finally, a filter system was added in the off gas module, and 99Mo would be extracted from the off gas. As long as the utilization percentage of 99Mo in the off gas module can reach 0.94%, the global demand under current data could be met, which implies a huge additional economic value for the SM-MSR.