Abstract: Ionospheric scintillation adversely impacts Beidou(BD) and its regional augmentation system. Making simulation with scintillation effected BD system performance models is the effective way to evaluate the availability of BD services under scintillation condition. A set of models, including the ionospheric scintillation affected receiver models, user positioning algorithms and system performance models are constructed in the paper. A combination of the scintillation distribution from global ionospheric scintillation model(GISM) and established models make it possible to analyze the system performance of BD and its augmentation system under scintillation condition. Simulation was conducted with the method to assess the service availability of BD augmentation system during the strong scintillation condition.It is found that the errors of receiver measurements will increase, and the system service availability will be degraded to a level of 95% or even less in low latitude areas of China where strong scintillation could happen. The low availability areas correspond closely to the areas existing strong scintillation.