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Using longer pseudo-random code in spread spectrum communication system can provide many benefits, such as improving the security of communication, increasing the ambiguous distance of pseudo code ranging. But it has comparatively difficulty in code acquisition. In this paper, the disadvantages of traditional FFT acquisition algorithm are analyzed firstly. The correlation peak affects the acquisition at low signal to noise ratio under the influence of the initial phase of pseudo code. To this problem, an improved FFT fast acquisition algorithm is proposed, which uses two channels correlation results to make acquisition. It can increase the detecting probability, and solve the problem of acquisition at low noise carrier to noise ratio. The FFT transform result of local pseudo code is stored in ROM to reduce the computational complexity and make it more suitable for hardware implementation. Finally the performance of the algorithm is analyzed, and the results of FPGA simulation are presented.