Abstract: To address the issues of low localization accuracy and lack of robustness for long-range and shallow sources within the deep-water near-seafloor shadow zone, a single-hydrophone source localization method based on the frequency-mode order domain mapping is proposed. Multipath signals with proximal arrival times after multiple bottom reflections are treated as a multipath group, and the source range is estimated by matching the time delay differences between these groups. Subsequently, a frequency-order domain mapping is constructed to eliminate the differences in the frequency-domain interference structures among different multipath groups. Characteristic time delay differences influenced by the source depth are extracted from the mapped signals, thereby achieving depth estimation. Unlike conventional methods that utilize only the first four rays, the source position information contained in all observed multipath groups is fully exploited in this method. Consequently, the problem of significant degradation in localization performance for long-range and shallow-depth source scenarios is effectively addressed. As validated by sea trial data, within the near-seafloor shadow zone at range of 60–80 km, the root mean square error (RMSE) of the horizontal range estimation for explosive sources at depths of 50 m and 200 m are 2.65 km and 2.26 km, respectively. The RMSE for source depth estimation are 4.10 m and 5.85 m, respectively.