During construction and operation, it is inevitable to have such engineering problems as cutoff wall defects. It is very important to accurately and systematically analyze the influence of defects in anti-seepage wall on seepage and deformation of cofferdam. The finite element model of an anti-seepage wall cofferdam project was established. By using the fluid-solid coupling analysis method, the material parameters of anti-seepage wall element in the finite element model were changed one by one to simulate different defects of anti-seepage wall. The influence of defect location of anti-seepage wall on saturation line, velocity vector field and deformation field of cofferdam was studied. The results show that the bottom defects of the anti-seepage wall have little influence on the saturation line, velocity vector field and deformation field of the cofferdam. With the upward movement of the anti-seepage wall defects, saturation line, pore water pressure and deformation value of the cofferdam behind the anti-seepage wall increase continuously, and the velocity of the cofferdam increases firstly and then tends to be stable. The research results can provide reference for the design and construction of anti-seepage wall and stability analysis of cofferdam.