Ship waterway tunnels are a new and special type of navigation facility that has emerged in the construction of complex hubs in high mountain valleys and rivers, and they have demonstrated broad applications worldwide. Due to their characteristics of long length, a dim visual background, and enclosed space, waterway tunnels are prone to causing tension and cognitive fatigue in ship officers on watch, affecting their decision-making and control abilities. This study constructs the visual navigation environment of a typical waterway tunnel in China using a ship maneuvering simulator. By monitoring the physiological data of ship officers, such as through electroencephalograms (EEGs) and electrocardiograms (ECGs), the temporal and spatial patterns of their physiological and psychological characteristics are analyzed systematically. Based on this, a quantitative model of the cognitive load of a ship officer working in a waterway tunnel is constructed. At the same time, the navigation risk of waterway tunnels of different lengths is quantized based on the entropy weight TOPSIS method, and finally, high-risk sections in waterway tunnels are identified and visualized, providing theoretical support for the management of safety in waterway tunnels.