The risk level of the Aids to Navigation (AtoNs) can reflect the ship navigation safety level in the channel to some extent. In order to appreciate the risk level of the aids to navigation (AtoNs) in a navigation channel and to provide some decision-making suggestions for the AtoNs Maintenance and Management Department, the risk assessment index system of the AtoNs was built considering the advanced experience of IALA. Under the Formal Safety Assessment frame, taking the advantages of the fuzzy comprehensive evaluation method, the fuzzy-FSA model of risk assessment for aids to navigation was established. The model was implemented for the assessment of aids to navigation in Shanghai area based on the aids to navigation three-dimensional simulation system. The real-time data were extracted from the existing information system of aids to navigation, and the real-time risk assessment for aids to navigation of the chosen channel was performed on platform of the three-dimensional simulation system, with the risk assessment software. Specifically, the deep-water channel of the Yangtze River estuary was taken as an example to illustrate the general assessment procedure. The method proposed presents practical significance and application prospect on the maintenance and management of the aids to navigation.