As a kind of special weak interlayer, the shear zone has aroused attention and a deep understanding of the influence on engineering construction. Shear zones of Guxian hydro-junction have some typical characters, such as long geological history, complex rock mass multiplex structure, and large-scale spread. From the perspectives of the lithologic combination, material foundation, and sedimentary structure, the development and spatial distribution characteristics of the shear zone are analyzed comprehensively in the dam site. Research results show that there are 12 layers of main shear zones in the rock mass of the dam site, including 2 layers at dam abutment and 10 layers at dam foundation. The distribution probability of each layer varies greatly, and JQD06 has the greatest influence on the stability of the dam foundation. Based on laboratory and in situ tests, this paper analyzed the mineral composition, chemical composition, and shear strength parameters of the shear zone in depth. Research results can be used to guide the evaluation of engineering geological conditions and the stability analysis of dam foundation rock mass in the similar area.