The damage assessment of aircraft carrier under the attacking of shrapnel is studied. Firstly, according to an analysis of the structure of shipboard aircraft support system and the vulnerability of the main facilities, a model of damage assessment is given by using Fuzzy Analytic Hierarchy Process (FAHP). Then, triangular fuzzy number complementary judgment matrix and reciprocal judgment matrix are used to determine the weights of the main facilities, sub-facilities and the comprehensive damage value, based on which the damage degree of the system is evaluated. Finally, according to the attack effect of a certain type of shrapnel, a damage assessment example is calculated out. The result shows the validity of the algorithm, which reflects that the carrier damage assessment is dependent on the changes of the system's operational effectiveness.