The East China Sea, situated at the intersection of the Eurasian, Philippine Sea, and Pacific plates, is characterized by complex geology influenced by tectonic phenomena such as plate movements, volcanism, faults, and uplifts. Crustal density structure inversion provides a thorough understanding of the region's geological history as well as Earth's dynamical evolution, providing critical insights into seismic disaster mitigation, resource exploration, marine environmental protection, and maritime safety. The inversion process, on the other hand, presents challenges in data quality, quantity, model complexity, uncertainty, and computational resources. With the advancement of next-generation satellite gravity measurements and developing inversion techniques, the inversion of marine crustal density structures promises to be more precise and comprehensive. We explored the density distribution in the East China Sea and surrounding areas using an innovative wavenumber domain three-dimensional density imaging method along with high-precision global satellite gravity data. By overcoming data quality and computing resource constraints, wavenumber domain three-dimensional density imaging has transformed the discipline of marine geophysics, successfully delivering accurate density distributions in the study area. We were able to get a more precise and comprehensive characterization of the crustal density structure by combining high-precision satellite gravity data and cutting-edge imaging methods. Our investigation has unveiled previously unknown details about density distribution in the East China Sea and its environs. The East China Sea shelf displays smooth low-density perturbations at 18 km depth, whereas the trench–arc–basin region exhibits increasing density perturbations. Notably, the Okinawa Trough, which is surrounded by the Tokara Volcanic Ridge and the Ryukyu Trench, displays strong positive anomalies with a north–northeastern to northeastern orientation. In contrast, the Ryukyu Ridge and the Philippine Sea Basin exhibit smaller negative values and substantial northwestward positive density trends, respectively. These findings indicate diverse material distribution, which provides important insights into the area’s geological evolution and tectonic processes. This study adds new insights into density distribution in the East China Sea and adjacent regions, offering information on the geological complexity of the region. The research lays the groundwork for future research on crustal dynamics and enhances the field of marine geophysics and related disciplines.Graphical abstract