The GPS multipath signal model is given and analyzed. The all phase DFT (apDFT) is proposed as a new spectral analysis way, which makes full use of (2N ¡ 1) samples to do linear transform into N point se- quence called all phase signal. Phase di®erence method is integrated with apDFT to determine the accurate signal frequency through calculating the two phase value for the two sequences' DFT result, i.e. one is from point 1 to point (2N ¡1) and the other is from (N +1) to (3N ¡1) separately. The application of the proposed method on GPS multipath signal estimation is analyzed, which has multiple frequen- cies components. Monte Carlo simulation results based on GPS simulator data show that the apDFT and the integra- tion with phase di®erence method could give the accurate frequency and precise phase estimation in both ideal and noisy environments.