Abstract: Due to the presences of a large number of buildings in ports and other areas, the navigation radar signals detected by specific emitter identification devices are affected by serious multi-path effects. In order to solve the above problems, a radar reference clock cycle feature extraction method is proposed in this paper, and based on this feature, the specific emitter identification of navigation radar is conducted in a harsh propagation environment. For the four quantum range working modes of two S-band navigation radars, the validity of radar repetition interval signature extraction is verified, and a linear classification model is constructed to verify the recognition validity, which verifies the effectiveness of the specific emitter identification method based on the base clock cycle feature against harsh propagation environment.