This paper proposes a dynamic identification method based on system modes to identify the stiffness of the duplex suspension clamp in the engine hydraulic pipeline. The hammering method measures the free modes of seven groups of duplex suspension clamp-double pipe (DSC-DP) specimens (including the same diameter and different diameters). The results show that the angular stiffness of duplex suspension clamp (DSC) is related to the first and fifth modes, and the line stiffness is related to the second and sixth modes. The dynamic model of the double pipe system with duplex suspension clamp is established by the dynamic stiffness matrix (DSM) method. The approximation function between the theoretical and the experimental frequency of the duplex suspension clamp is established to reverse the stiffness of the duplex suspension clamp. The frequency response function (FRF) of the system theory and the experiment is predicted according to the results of the reverse stiffness. The coincidence of the frequency results verifies the correctness of the proposed method. Moreover, the validity of the stiffness of the duplex suspension clamp is verified by comparing the frequency results obtained from the theory, experiment, and finite element method (FEM) under the free and fixed boundary conditions. The method of identifying the stiffness of duplex suspension clamp and the obtained stiffness in this paper can provide positive guidance for the vibration analysis and modal test of aero-engine pipelines.