Abstract: With the rapid development of satellite navigation systems, high-precision and trustworthy navigation based on low earth orbit (LEO) satellite has become a hot topic in current research. However, the safety and trustworthiness issues of LEO satellite navigation have always hindered its large-scale application. The authentication scheme based on spreading code and navigation data based authentication proposal (SNAP) has shown a good trend in solving the above problems. The focus of this paper is to solve the intermittent tracking algorithm and performance analysis of SNAP signals, and obtain the analytical expression of tracking error. The research results show that the error accumulation caused by intermittent tracking follows a Gaussian distribution, and its mean is proportional to the Doppler frequency shift rate, and the variance is equivalent to the loss of carrier-to-noise ratio. Compared with the carrier loop, the code loop is less affected by Doppler. The research results of this paper provide important theoretical reference for the design of receiver system parameters under intermittent tracking structure.