Abstract:   Rapid and random temporal fluctuations in amplitude and phase of GNSS signals caused when they are propagating through irregularities in electron density of the ionosphere are called ionospheric scintillation. Ionospheric scintillation has some influence on the receiver signal acquisition, tracking, demodulation and positioning. In this paper, the influence of ionospheric scintillation on I,Q branch and tracking loop is analyzed by theoretical and simulation methods. The results show that the phase scintillation has an effect on the signal I Q branches, and the amplitude scintillation has a great effect on the I branch. In the place where the phase scintillation is stronger or the Amplitude scintillation is stronger, the signal is more difficult to track. In weak scintillation conditions, the tracking threshold of PLL is about 29 dBHz,and the tracking threshold of DLL is about 20.2 dBHz. In strong scintillation conditions, the tracking threshold of PLL is about 32dBHz,and the tracking threshold of DLL is about 22 dBHz. In contrast, the carrier tracking loop is more fragile. At the same time, the stronger the scintillation, the greater the probability of the carrier cycle slip, the higher the carrier to noise ratio, the stronger the anti-scintillation ability.