Due to its accidental, sudden and regional characteristics, the simulation of GNSS navigation signals under ionospheric scintillation is difficult to be implemented accurately. The ionospheric scintillation time-series generation method based on Gamma distribution and zero-mean Gaussian distribution was proposed. With the NSS8000, a multi-system navigation signal simulator developed by our department, the hardware architecture of BeiDou navigation signal simulation under ionospheric scintillation was given. Then based on this, by intermediate frequency signal sampling and software receiver processing, the impact of ionospheric scintillation on BeiDou receiver tracking loops was analyzed. The results indicate that the code tracking error can reach 0.05 chips when the phase scintillation index is 0 and amplitude scintillation index is 0.9, while the carrier tracking error can reach 15 degrees when the amplitude scintillation index is 0 and the phase scintillation index is only 0.5, which the carrier tracking loops is almost loss of lock.