Electromagnetic detection arrays installed on the seafloor can be utilized not only for oil and gas exploration but also for detecting extremely low-frequency electromagnetic signals emitted by ships. These signals are generated by the periodic changes in contact resistance within the ship’s shafting structure, resulting in frequencies that are closely tied to the propeller’s rotational speed. As they encode information about the vessel's operating status and position, they are of great importance in underwater detection. However, the extremely low signal-to-noise ratio and the abundance of interference sources in complex marine environments make it difficult for conventional methods to achieve stable detection and effective extraction of such signals. To address these challenges, this paper presents an innovative joint detection method for extremely low-frequency electromagnetic signals based on an improved time-frequency phase difference spectrum. By designing an exponential weight mask, phase difference information is transformed into a dimensionless, integrable weight. Additionally, the time-frequency coherence between orthogonal magnetic field components is incorporated, enabling deep integration of phase features and power spectra in the time-frequency domain. This significantly improves both the utilization and clarity of signal characteristics. Simulation tests and real-world sea trial data demonstrate that the proposed method excels at detecting extremely low-frequency electromagnetic signals and suppressing noise. Compared with traditional time-frequency analysis techniques, this approach offers clear advantages in signal separation and feature enhancement, providing a reliable technical solution for electromagnetic detection of ships in complex marine environments and offering substantial engineering value.