To obtain a high-accuracy position with SINS(Strapdown Inertial Navigation System), initial alignment needs to determine initial attitude rapidly and accurately. High-accuracy grade IMU(Inertial Measurement Uint) can obtain the initial attitude indenpendently, however, the low-accuracy grade gyroscope doesn't adapt to determine the heading angle, hence the initial attitude matrix will not be obtained. If using large misalignment angle model to estiamting heading angle, the convergence time will become much longer. For solving these two problems, a novel alignment algorithm combined backtracking algorithm and reverse navigation updating method with GNSS(Global Navigation Satellite System) aiding is proposed herein. The simulation and land vehicle test were finished to evaluate the alignment accuracy of the proposed algorithm. The horizontal misalignment is less than 2.3 arcmin and the heading misalignment is less than 10.1 arcmin in test. The proposed algorithm is a feasible and practical alignment method for low-cost IMU to obtain initial attitude in short term and large misalignment condition aided by GNSS.