Aircraft or ships are often interfered by strong electromagnetic radiation during navigation, which always causes seriously damage to their electronic equipment. Quantitative analysis of these effect is essential to the design of the electronic system. In the past decades, case by case analysis has been reported in many publications. With the rapid progress of big data and machine learning algorithms, it is possible to adopt these new technologies to analyze this problem. Data is the key in big data technology, however, there is no database design has been reported for strong electromagnetic radiation effect data. To serve this problem, this paper proposes a design scheme of strong electromagnetic radiation effect database system based on relational database. In this system, the software part adopts modular design to improve the flexibility and scalability of the system; the authentication module and log module are introduced to ensure the security and stability of the database; the machine learning module is designed to provide the ability of system data analysis, and finally a relatively complete database system is developed for strong electromagnetic radiation effect.