The anti-seismic performance of a skip floor shear wall structure and a traditional shear wall structure are analyzed, the influence of the skip floor shear wall structure form is analyzed, the three-dimensional calculation models of two skip floor shear wall structures and the traditional shear wall structure are respectively established, finite element software Ansys is adopted to calculate the earthquake response analysis of the models, and the structure displacement time interval curves and stress distribution characteristics of the skip floor shear wall structure and the traditional shear wall structure under the earthquake effect are obtained, the calculation result shows that the stress distributions of the three structures are similar, the displacement of the skip floor shear wall structures is bigger than the displacement of traditional shear wall structure under three different earthquake effects, however, the skip floor shear wall structures still can satisfy the demands of lateral sway in regulations and explains that the skip floor shear wall structures can be used in project practice.