Abstract: Aiming at the BeiDou Navigation Satellite System/inertial navigation system (BDS/INS) deep integrated positioning system, a signal tracking algorithm using inertial nartgation system (INS) assisted B1C orthogonal component is proposed to solve the problem of lock-out of the deep integrated positioning system caused by weak signal in the positioning process. The algorithm uses the Kalman filter algorithm considering the inertial navigation data, at the same time, it uses the pilot component and data component to form a local code to track the signal. The algorithm is used to calculate the measured data, and compared with the traditional algorithm. It can be concluded that the tracking loop is more stable in the weak signal environment, the positioning accuracy is significantly improved, and the pseudo range also has a higher accuracy.