The configuration and aerodynamic performance of the inlet system are important aspects in the process of installing a gas turbine on a naval vessel. Under the requirements, large eddy simulation (LES) is used to simulate the three-dimensional fluid flow in the wave blocker of a marine inlet filter. The Smagorinsky-Lilly sub-grid model was used to model motions of small-scale structures. During numerical simulation, the SIMPLE algorithm was applied. The central-differencing spatial discretization scheme and the second order accuracy finite difference for the temporal discretization were used. Simulation gives satisfactory distribution of the vorticity fields and turbulent kinetic energy.Compared with the k-ε turbulent model, the results of LES are better for the distribution of parameters. The results of experimental study in a small-scale wind tunnel indicate that numerical calculation has higher accuracy. Therefore, the methods used are worthy of reference and introduction for the design of an inlet system.