Anti-seepage wall is an important anti-seepage structure in cofferdam, which plays an active role in improving the distribution of seepage field and the stability of cofferdam. This paper presents an optimization method of cutoff wall structure based on artificial fish optimization algorithm. Taking a cofferdam project as an example, the calculation model of cofferdam was established based on finite element analysis, and the wall thickness and rock depth of cutoff wall were taken as the variables to be optimized. Finally, the safety factor of cofferdam under the condition of constant water level and sudden drop of water level was obtained through seepage and stress coupling analysis. Compared with the traditional artificial fish swarm algorithm, the results show that the optimized method based on the improved artificial fish swarm algorithm has faster convergence speed and convergence accuracy, and the optimized anti-seepage wall structure can achieve the balance between the anti-seepage effect and the economy. The pore water pressure behind the cutoff wall decreased significantly, and the safety factors of the cofferdam under the conditions of constant water level and falling water level (falling rates are v=0.5 m/d, 1.0 m/d and 2.0 m/d, respectively) were 1.489, 1.410, 1.376 and 1.321, which met the safety requirements, reflecting the feasibility and rationality of the proposed method. The research results can provide reference for the design and construction of cofferdam.