Using exclusively for civil aviation system, GPS (Global Positioning System) L5 signal is set up and takes up an appointed frequency band. However, the DME (distance measurement equipment) signal which has already applied for distance measurement in the civil aviation system works as the same frequency band as GPS L5 signal. As a forced high-power pulse interference, DME signal will decrease SINR (signal-to-interference and noise ratio) of GPS L5 signal and even give rise to failure of acquisition and tracking. In case the DME interferences come from more than one base station, the traditional DME interference suppression methods which bring about the loss of GPS signal will suffer from serious performance degradation. In the light of the received signal model, a new DME interference mitigation algorithm is presented in this paper. At first, frequency is estimated with tmwapDFT (time-modulated windowed all-phase DFT). Then, we use the estimated frequency to get amplitude and signal delay information by signal separation estimation theory. In addition, we consider the previous estimated results as the initial value, and a two-dimension search method is implemented in a small range for further improving the parameter estimation accuracy. Based on the estimated parameters, DME signal can be exactly reconstructed and then eliminated. It can be shown from the experiment results that the proposed method which keeps more useful signal has a better performance compared with the conventional ones.