To solve the problem how to prevent the marine environment monitoring feature data from leaking when an emergency occurs, a destruction of data used in marine environment monitoring buoy system is researched. The architecture design of the system is introduced; a data overwrite algorithm based on the data secret level of the marine work is proposed; through data overwrite technology and the high-pressure circuit to achieve the safe destruction of data elements in marine environmental monitoring. The study shows the data destruction system can trigger data destruction procedures in real time, it can solve data security issues for marine environmental monitoring buoy in the out of control situation, and the destroyed data is unrecoverable, thus preventing data loss and leakage.