Proposed in this paper is a novel method of M-ary orthogonal spread spectrum, with which the potential periodicity of transmitted signals is eliminated and the data are hard to detect or intercept. Thus, both the anti-jamming and the anti-intercept capabilities of the system are well guaranteed. In the condition of long pseudo code and large carrier Doppler frequency shift, the number of FFT points in the conventional synchronous acquisition algorithm is too large, the complex multiplication is of high computational complexity and large time cost, and the parameter evaluation acquired in a long duration is not applicable for carrier tracking because it is too old. In order to solve these problems, an improved fast synchronous acquisition algorithm is proposed, which helps to search for the code synchronization point and estimate the cartier frequency offset for correction, with the computational complexity obviously reduced.