In view of the existing problems such as complexity in solving navigation safety degree of ships and difficulty in determining the weight of reference factors, etc, by studying the sources of the data and model construction methods that affect the accuracy of the estimation model. This paper presents a method of selecting key indicators of ships based on relational database and a design scheme of database construction and retrieval, constructs a ship collision risk solving model based on fuzzy mathematics, analytic hierarchy process (AHP) and expert grading method. The accuracy of the database and the estimation model of ship navigating safety is verified by the ship AIS data. The results show that the database based on AIS data has commendable reliability and ease of use, and the calculated results of the estimation model of ship navigating safety are reliable, which conforms to the requirements of expert experience and International Regulations for Preventing Collisions at Sea,1972, and provides a reference technical route and method for the ship navigation safety evaluation.