Low-visibility environments induced by sea fog severely constrain the navigational efficiency and safety in narrow waterways, where traditional radar and Automatic Identification Systems (AIS) frequently encounter challenges such as perception blind spots and information lag. To address this critical issue, this study proposes a UAV-based perception and decision-making methodology for main navigational routes in fog, integrating physical priors with unmanned aerial vehicle (UAV) vision. Firstly, a joint physical dehazing and fog-domain adaptive detection network is constructed. This network addresses the overcomes the interference of non-uniform fog through feature-level enhancement, generating a spatio-temporally continuous visibility field and ship probability grids under a bird’s-eye view (BEV). Subsequently, a quantified “Sailability Score” model is established, providing a scientific basis for the dynamic diversion, speed limitation, and safe distance maintenance of main navigational routes. Simulation-based verifications using real-world fog navigation scenarios in the Qiongzhou Strait, coupled with a joint analysis of Vessel Traffic Service (VTS) and AIS data, suggest that at the critical visibility threshold (≤500 m), the proposed method improves the recall rate of long-distance small target detection by approximately 16.2% and reduces the visibility estimation error by 19.3%. Furthermore, the consistency between the proposed Sailability Score and the actual VTS navigation restriction windows reaches 82.1%, exhibiting a conservative preference for safety (i.e., risk preference ratio (Formula presented.)). Additionally, by introducing a temporal anti-jitter mechanism (parameterized by a smoothing window (Formula presented.)), the proposed method extends the navigable time window of the main routes by approximately 12.4% while ensuring navigational safety. The simulation results indicate the framework’s potential perception capabilities and engineering applicability, providing reliable technical support for smart shipping and intelligent VTS systems.