The protection of aircraft or ships from strong electromagnetic radiation is a key issue during their navigation. With the repaid development of big data technology, it is possible now design the hardware under the guidance of database. However, it is always lack of specific database. In this paper, strong electromagnetic protection database system design is employed to predict the damage effect. Based on this design scheme, the database is designed according to the third normal form; The software part adopts modular design to improve the flexibility and expansibility. The results demonstrate the ability of system data analysis by designing machine learning module, and finally forms a powerful electromagnetic protection database system with relatively perfect function.