Navigation database can be used for navigation calculation and automatic tuning management of navigation platform, etc. It is necessary to flight management system data sources. In order to effectively improve the efficiency of the use, update and maintenance of the onboard navigation database, greatly reduce the workload of the relevant staff, the fast parsing and generating method of airborne navigation database based on relation model is proposed. Modeling a large number of data objects contained in the ARINC424 protocol to define logical relationships and constrains between objects in the protocol, and optimizing the data structure, establishing a cross-reference relationship between the data through the intermediate relationship table, thereby fast parsing and generating of the database is realizing. The test results show that the method can effectively improve the efficiency of data query, reduce the time consumption of data parsing and generating, and make the database performance better.