Ships are often suffered from uncertain strong electromagnetic environment radiation during navigation, which always cause certain damage to their electrical equipment through coupling. In order to study the correlation characteristics between strong electromagnetic environment and damage characteristics, for the problems of information complexity and uncertainty in them. In this paper, the correlation analysis about complexity of their damage characteristics based on grey correlation is proposed. Combined with the physical characteristics of strong electromagnetic environment parameters, the correlation model of the corresponding coefficients is established, which shows that the model can find the main influencing factors from incomplete information. Thus, it can provide a effective solution for the strong electromagnetic protection process, improve the protection efficiency, verify the feasibility of this method through the measured data, and provide a better solution for the electromagnetic protection process in the future.