Quality of seismic data for basin-mountain transition zone in middle part of western Sichuan Depression is poor. So, there is ambiguity in structure interpretation. Based on outcrop, drilling and seismic data, this paper considers that the stratified deformation structure is more reasonable. Analysis of structure evolution shows that the activity of Anxian-Guanxian Fault is representative in Late Indo-Chinese epoch, the activity of nappe structure is strong and horizontal contraction is large. Structure deformation is weak in early Yanshanian epoch. In Mid-Late Yanshanian and Himalayan epoch, Guankou Fault developed and horizontal contraction was small, which associated with obvious basement uplift.