Wrinkles in geomembrane are common among anti-seepage engineering. However, the wrinkling effect has been neglected in most of the current studies on the interface shear properties of geomembrane. The composite liner consisting of a textured geomembrane (GM) and a needle punched geosynthetic clay liner (GCL) was taken as the research object, and the hydration deformation tests confirmed that the two-step hydration method was effective in accelerating the hydration of the wrinkled GM+GCL composite liner. The shear properties of the wrinkled GM+GCL composite liner was studied by a large-scale temperature-controlled submerged direct shear apparatus. The shear characteristic of the wrinkled GM+GCL composite liner was analyzed compared to the shear results of the composite liner without GM wrinkle, and the influence mechanism of GM wrinkles on the shear characteristics of the composite liner was clarified. Experimental results show that the existence of GM wrinkle will change the shear stress– displacement curve of the GM+GCL composite liner a lot, and the peak shear strength of the composite liner under low normal stress can be obviously reduced by the GM wrinkle. Significant progressive failure could be observed in the wrinkled GM+GCL composite liner. Additionally, multiple failure modes can coexist inside the composite liner under unique normal stress as well.