The major weakness of global navigation satellite system receivers is their vulnerability to intentional and unintentional interference. Frequency domain interference suppression (FDIS) technology is one of the most useful countermeasures. The pseudo-range measurement is unbiased after FDIS filtering given an ideal analog channel. However, with the influence of the analog modules used in RF front-end, the amplitude response and phase response of the channel equivalent filter are non-ideal, which bias the pseudo-range measurement after FDIS filtering and the bias varies along with the frequency of the interference. This paper proposes an unbiased interference suppression method based on signal estimation and spectrum compensation. The core idea is to use the parameters calculated from the tracking loop to estimate and reconstruct the desired signal. The estimated signal is filtered by the equivalent filter of actual channel, then it is used for compensating the spectrum loss caused by the FDIS method in the frequency domain. Simulations show that the proposed algorithm can reduce the pseudo-range measurement bias significantly, even for channels with asymmetrical group delay and multiple interference sources at any location.