<p>To address the challenge of detecting small underwater targets, this paper proposes a detection method based on the fusion of acoustic and magnetic fields. The shaft-rate acoustic field and shaft-rate magnetic field of a vessel are both closely related to the rotation of its propeller and contain rich target characteristic information. Using the vessel’s shaft-rate information as a key criterion, this paper proposes to fuse the acoustic and magnetic fields to extract the shaft-rate features of the vessel. Specifically, the line spectra of the shaft-rate acoustic and magnetic fields are first extracted using DEMON spectral analysis and power spectral analysis methods, respectively. Subsequently, the extracted line spectra are fused and purified. Finally, the shaft-rate features are extracted based on the greatest common divisor (GCD) method. To verify the effectiveness of the proposed method, real-measured acoustic and magnetic data from multiple vessels were used for experimental validation. The results show that there is a significant frequency correspondence between the line spectra of the shaft-rate acoustic and magnetic fields of the same vessel. By fusing the shaft-rate related line spectra of the acoustic and magnetic fields, the problem of line-spectrum loss in a single physical field, caused by environmental noise and other factors, can be effectively compensated. Moreover, after fusing the acoustic and magnetic fields, the accuracy and stability of the vessel’s shaft-rate estimation are significantly better than those of a single physical field, allowing for more reliable extraction of shaft-rate information and enhancing the basis for target identification.</p>