Mortise-tenon (M-T) joint, column foot joint, and Dou-Gong joint play a key role in the seismic behavior and energy dissipation of traditional timber structures. To simplify the modeling process and predict accurately the hysteretic behaviors of traditional timber joints as well as the global seismic responses of traditional timber structures, three types of composite elements, which were composed of varying non-linear one-dimensional spring elements available in the ANSYS finite element (FE) software, were proposed to characterize the hysteretic performance of the M-T joint, the column foot joint, and the Dou-Gong joint, respectively. The beam element was used for simulating the timber components with large size and not easily damaged. The parameters of the composite elements were identified from the simplified hysteretic model or test hysteretic curve of each type of joint. The simplified FE models of the M-T joint, M-T jointed timber frame, column foot joint, and Dou-Gong joint were developed, and verified using the cyclic loading tests of joints, respectively. Based on the validated composite elements and simplified FE models of varying joints, the three-dimensional simplified bar system FE model of a 1/3.52-scaled palace-style ancient timber structures was established using the ANSYS, and also validated using the shaking table tests, in terms of its dynamic characteristics and responses. Good agreements between the model predictions and test results were observed. Additionally, parametric analyses were performed, while revealing and quantifying the effects of performance degradation for the M-T joint, column foot joint, and Dou-Gong joint on the dynamic responses to the structure. It is found that the damage to the Dou-Gong joint had little effect on the maximum story drift of column frame layer, however, the damage to the M-T joint and column foot joint would significantly increase the maximum story drift of column frame layer. When the damage degree of the M-T joint, Dou-Gong joint, and column foot joint in the structure was up to 60%, the maximum story drift ratios of column frame layer were close to 1/48, 1/50, and 1/39, respectively, the maximum story drift ratios of Dou-Gong layer were approximately 1/164, 1/98, and 1/125, respectively.