Understanding the multi-cage interaction mechanism in fish cage arrays and the hydrodynamic behaviour of cage structures will help engineers explore the feasibility of offshore fish farming. In this study, a semi-analytical method is developed to simulate the wave response of an array of cylindrical fish cages with arbitrary layouts and dimensions, including the wave interference effects among the multiple cages. By eigenfunction expansions, the general solution of the present research problem is expressed in the form of a Fourier-Bessel series, and the corresponding particular solution is obtained by introducing relevant boundary conditions and the least-squared method. The simulation results show that significant wave effects occur at the top of the cages, and the dynamic response of each cage has obvious phase differences. Parametric studies on the wave forces show that the wave force is zero at a specific wave frequency and the wave forces are decreased under high porosity nets.