The invention discloses a tracking method and a tracking system for high dynamic GNSS carrier wave signals. The tracking method comprises steps of initial demodulation and pre-detection integration; estimation on a Doppler frequency of a present carrier wave signal and an acceleration speed in a satellite direction; secondary demodulation; carrier wave phase detection and navigation text extraction; loop update and re-demodulation. The tracking system comprises a first carrier wave voltage control oscillator, a pre-detection integrator, a fractional order Fourier converter, an acceleration speed estimator, a high dynamic frequency monitor, a second carrier wave voltage control oscillator, a phase monitor and a tracking filter. According to the tracking method and the tracking system, the extremely high dynamic carrier wave signals can be tracked by a receiver, restriction of a loop bandwidth on dynamic tracking capability is released, influence of dynamic levels on detection is reduced, tracking loop design is simplified, and a use scope of a GNSS receiver based on Beidou/GPS is expanded.