In view of the existing shortcomings such as complex solution of ship navigation safety degree at sea and difficult weight determination of reference factors, etc., the problems such as data sources and model construction methods that influence the accuracy of evaluation model are studied, a ship important index screening method and a design scheme of database construction and retrieval are proposed based on the relational database. A ship collision risk solution model based on the fuzzy mathematics method, Analytic Hierarchy Process (AHP), and expert evaluation method is constructed, and the ship navigation safety evaluation mathematical model and constructed database are verified according to the real ship Automatic Identification System (AIS) data. The results show that the ship navigation safety evaluation database based on the AIS data is of better reliability and usability. The calculation results of ship navigation safety evaluation model are reliable and accord with the expert experience and the requirements of The International Regulations for Preventing Collisions at Sea 1972, which can provide technical and theoretical support for the evaluation of ship navigation safety at sea.