In this study, we propose a novel method for retrieving the three-dimensional (3D) wave surface from sea clutter using both simulated and measured data. First, the linear wave superposition model and modulation principle are employed to generate simulated datasets comprising 3D wave surfaces and corresponding sea clutter. Subsequently, we develop a Pix2Pix model enhanced with a self-attention mechanism and a multiscale discriminator to effectively capture the nonlinear relationship between the simulated 3D wave surfaces and sea clutter. The model’s performance is evaluated through error analysis, comparisons of wave number spectra, and differences in wave surface reconstructions using a dedicated test set. Finally, the trained model is applied to reconstruct wave surfaces from sea clutter data collected aboard a ship, with results benchmarked against those derived from the Schrödinger equation. The findings demonstrate that the proposed model excels in preserving high-frequency image details while ensuring precise alignment between reconstructed images. Furthermore, it achieves superior retrieval accuracy compared to traditional approaches, highlighting its potential for advancing wave surface retrieval techniques.