Ionospheric scintillation is a rapid change in the phase and amplitude of navigation signals, resulting in degraded accuracy and robustness of signal tracking loops. Compared with the frequency tracking loop and delay tracking loop, carrier tracking loop is much weaker, and will lose lock much more continually in scintillation. Therefore, a carrier tracking algorithm for BeiDou signals scintillation mitigation based on adaptive EKF (extended Kalman filter) was proposed. The integration of in-phase and quadrature channels was used to estimate the phase lock indicator values which are the control parameter to adjust the measurement vector of EKF adaptively with different scintillation scenarios. Through the adaptive measurement vector, the accuracy and robustness of the tracking can be improved and the probability of filter divergence can be decreased. Experimental results prove the validity of the analysis and the proposed carrier tracking algorithm.