Geosynthetic Clay Liner (GCL) is a new type of material commonly used for lake bottom seepage prevention, but if the roots of lake aquatic plants penetrate into GCL, it affects its seepage prevention effect. In order to explore the influence of GCL's hydraulic conductivity under the penetration of plant roots, model tests were carried out on plants such as Thalia dealbata, reed, and cattail, GDS (global digital systems) geoenvironmental permeameter was used to test the hydraulic conductivity of GCL after the penetration of aquatic plant roots. The results show that: (1) Under the same confining pressure, with the increases of the penetration rate of plant roots, the GCL hydraulic conductivity under the penetration of Thalia dealbata, reed and cattail roots gradually increase, and the maximum increases to 10-7 m/s. (2) When the root penetration rate is greater than 1%, the GCL hydraulic conductivity of withered roots is about 1.26~3.13 times that of the normal roots morphology. The withered roots have a more significant impact on GCL permeability than the normal root morphology. (3) The roots of cattails and reeds have similar effects on the hydraulic conductivity of GCL, while the roots of Thalia dealbata have little effect on the hydraulic conductivity of GCL.