Aimed at the health problem of aqueduct support system, the paper proposed a method which determine the damage position of aqueduct support system based on the change rate of natural frequency. CFD(computational fluid dynamics) method was applied to calculate the natural frequency of the rectangular damaged aqueduct-water coupling body under the condition of different water depths. The results show that the condition of different water depths and degrees of injury do not affect regular rate of change frequency. Based on similarity theory, the fingerprint database was established to research the damage location of aqueduct support system. The results indicated that the method which uses fingerprint of the rate of change frequency of aqueduct to judge the damage location is feasible. The results provide a guideline for further study of aqueduct damage.