At present, the thunderstorm season has a greater impact on civil aviation, which can lead to an increase in operational safety problems. Currently, the central runway 36R instrument landing system (ILS) descent stage and the protected area located in the low-lying geographical location of Beijing Capital Airport are prone to flooding during the thunderstorm season, which can cause the equipment parameters to exceed limits and cause unsecured events that cause equipment shutdown and affect operations. This paper analyzes the unsecured event caused by flooding in the protected area of the 36R ILS descent stage during the thunderstorm season in 2022 and studies the reasons for the shutdown. Subsequent installation of rainfall monitoring software and other support measures will optimize equipment monitoring under the current conditions and avoid unsecured events. This paper provides a valuable experience for the inspection and resolution of navigation equipment problems in the summer thunderstorm season and provides valuable experience for the thunderstorm season.