The presence of complex electromagnetic noise in the ocean significantly impacts the accuracy of ship shaft-rate electric field signal detection, necessitating the development of an effective denoising method to enhance detection precision. Nevertheless, traditional denoising methods encounter issues like low frequency resolution, challenging threshold configuration, and mode mixing. This study introduces a method that integrates variational mode decomposition (VMD) with multi-window spectral subtraction (MSS). The intrinsic mode functions (IMFs) of noisy signals are extracted using VMD, and the noise components within different IMFs are identified. The spectral features of both signal and noise within different IMFs are leveraged to eliminate noise signals via MSS. Subsequently, the denoised components of IMFs are rearranged to derive the denoised ship shaft-rate electric field signals, achieving noise reduction across various frequency bands. Following validation using simulation signals and empirical data, the noise reduction efficacy of VMD-MSS surpasses that of alternative methods, demonstrating robust performance even at low signal-to-noise ratios. The marine electromagnetic noise is effectively suppressed in the empirical data, while preserving the characteristics of ship’s shaft-rate signals, thereby validating the method’s efficacy and demonstrating its practical engineering value.