Cross-sea bridges and tunnels play a significant role in alleviating transportation bottlenecks. Accurate and comprehensive geological survey data is essential for selecting and optimizing cross-sea transportation engineering plans, designing improvements, and formulating construction plans. It also serves as a vital safeguard for engineering risk decision-making. However, traditional survey methods face limitations in underwater tunnel projects due to the complex marine traffic environment, aquatic conditions, and variable topography and geology. This study, based on the Jintang Subsea Tunnel survey project for the Ningbo-Zhoushan Railway, introduces three-dimensional seismic exploration technology into the field of engineering surveys, exploring new approaches to surveying underwater tunnels under complex geological conditions. The application of three-dimensional seismic reflection in the Jintang Subsea Tunnel survey project solves the challenges associated with data collection in shallow water areas through a collection scheme that includes single-cable, parallel, and multi-line closely spaced acquisitions. Advanced processing techniques, such as tidal correction based on high-precision measurement data, multiple wavelet suppression techniques using pre-stack predictive deconvolution and post-stack wavefield extrapolation, and well-constrained depth conversion techniques, significantly improve the vertical and lateral resolution of three-dimensional seismic exploration in water areas and enhance the accuracy of survey results. This approach successfully addresses the spatial distribution of the seabed, Quaternary strata, and underlying bedrock (submarine mountains) in complex geological sections, as well as the range of structural features and fractured zones. Furthermore, the well-constrained geological modeling technique based on three-dimensional seismic reflection results accurately simulates the spatial contact relationships between formations and structures. By integrating engineering models, it enables a visual analysis of the geological conditions along the tunnel, effectively improving the quality of survey results and achieving high-precision three-dimensional geological exploration. The application study of the Jintang Subsea Tunnel survey project demonstrates the feasibility of high-precision three-dimensional seismic reflection exploration technology in water areas. It provides accurate and reliable geological survey results for water-based engineering geological surveys, design optimization, and engineering risk decision-making, offering a fresh perspective for complex engineering geological surveys in water areas and showing excellent practicality and potential for broader adoption.