Abstract: A seismic performance analysis of four concrete-filled steel tube columns is conducted with the weakened flanges and penetrated composite joints using three-dimensional solid finite element model. Besides the triaxial plastic damage of concrete and the isotropic-kinematic combined hardening model of steel tube, a ductile damage model of structural steel is introduced in the finite element analysis to accurately simulate the influence of steel beam weakening on the seismic behaviours and the failure mode of the joints. The results indicate that the proposed finite element model is more rational when comprised with the experimental observation. The effect of steel beam weakening reduces the stiffness, bearing capacity, and energy dissipation capacity of the joints. Meanwhile, the effects of the sizes of steel beam and column end reinforcing bars on the joint’s bearing capacity, stiffness, plastic energy dissipation allocation and failure mechanism were analyzed. The results show that when the ratio of the bending capacity, axial stiffness and the sectional stiffness of the beam and column ranges from 1.66 to 2.11,1.90 to 1.96 and 1.16 to 1.21, respectively, the major member of energy dissipation will shift from beam to the column in the penetrated joints. By setting stirrups at the column end, the bending capacity and energy dissipation of the joints were significantly improved due to the direct restraining of the concrete. The composite joints can maintain the beam end failure type even subjected to high axial compression. Hence in the Design Code, the ratio of the bending capacity of beam and column bending capacity ratio value is less than 1, which is a conservative definition for the strong column and weak beam penetrated joint.