Tracking procedure of DS/FH (direct sequence/frequency hopping) spread spectrum signal is effected by Doppler effect and ionospheric effect seriously, which makes it hard to be used for the anti-interference field of satellite navigation. To solve this issue, a recursive least square based filtering was proposed to improve this stability of DS/FH signal tracking. The carrier Doppler estimation with variable center frequency in different channel was converted to the estimation with the center frequency of the DS/FH signal and filtered, and the numerically controlled oscillator of carrier was revised according to the predicted Doppler frequency as the frequency hops. The total electron content was estimated in real time by observing the carrier phase and code phase mutations, and the carrier phase and code phase was revised as the frequency hops. Simulation experiments demonstrate the proposed method is effective to eliminate the frequency and phase discontinuity of the DS/FH signal tracking, whose tracking accuracy can be the same level as DS signal.