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To verify that the total least-squares method is a better suitable for fine synchronization than the least-squares method, propose the precise synchronization method based on the total least squares. This method is on the base of PN code’s BPSK modulation . After the receiver get the phase curve, to get the data of curve’s several fixed position near the zero point. then using the total least squares based on QR decomposition and singular value decomposition fitting out the phase line, and estimate the synchronization error. According to the result of the simulation in Matlab software, draw the conclusion:under the noise environment, the Total least squares method in the application of synchronous can be better than that of synchronization based on ordinary least squares method on measuring precision and stability. Especially under the condition of low signal noise ratio (SNR), based on the least squares of synchronous measurement precision is improved more than 3 times.and the stability performance is improved more than 5 times.