The seismic performance and failure mechanisms of the substation structure system considering dynamic interaction on the main structure and substructure was studied systematically, based on the mechanism of primary-secondary structure dynamic interaction, implicit dynamics numerical simulation analysis and shaking table test. Seismic response of the structure system was analyzed in some aspects such as internal force, displacement and acceleration. This paper obtained the interaction mechanism between the electrical equipment with main structure, the dynamic magnification factor of the electrical equipment and the dynamic property values, and put forward the seismic performance goals of the main structure. Meanwhile, the results based on the displacement revised factor method established the level damage assessment model and the overall damage assessment model, and then proved the correctness of the damage assessment model by shaking table test. These research results have important reference function on seismic design and seismic damage assessment of the similar lifeline engineering and industrial architectures with complex equipment.