Artificial reefs can be regarded as artificial structures in the sea. There are three methods to reflect bottom structures in large-scale ocean models: method of water depth modified treats artificial reefs as impermeable solids and reflects reefs by changing the water depth, which is applicable to impermeable reef mountains; method of bottom friction increased reflects the obstruction of water flow by structures on the seabed by increasing the bottom friction of the model, which is applicable to the simulation of submarine mussel beds and low oyster reefs; method of retarding force simulates the obstruction of water flow in different water layers by adding a retarding force term to the model momentum equation. In order to reasonably represent the permeable artificial reef assemblage in the large-scale ocean model, the hydrodynamic conditions of the proposed artificial reef area on Dachen Island were simulated based on the numerical ocean model FVCOM (An unstructured grid Finite-Volume Community Ocean Model), and the differences of vertical flow velocity, reef top plane flow velocity, upward transport flux and back eddy volume before and after reefing were compared among the method of water depth modified, method of bottom friction increased and method of retarding force. Based on the difference of flow velocity before and after reef casting, the empirical formula was applied to predict the bottom bed sediment flushing and siltation one year after reef casting. The numerical simulation results showed that by adding the retarding force term in the model, the flow velocity in the occupied water layer was reduced by 0.06 m/s compared with the time when the reef was not installed, and the maximum upward flow velocity was 0.005 m/s in the direction of incoming flow; the reduction of flow velocity at the back of the reef at the time of rapid rise can be more than 20 times of the combined length of the reef, and the maximum thickness of the bottom bed siltation after one year in the corresponding flow velocity reduction sea was about 0.05 m, the average upward water transport flux of single reef was 66 m³, and the back eddy volume was 1550 m³. Compared with the method of water depth modified and the method of bottom friction increased, the retarding force method can well represent the effect of the reef on water flow, avoiding the problem of overestimating the flow field effect in the simulation of permeable reefs by the method of water depth modified, and without the defect that the method of bottom friction increased is only applicable to low reefs. The hysteresis method is not only applicable to the bottom-set permeable reefs, but also to the study of hydrodynamics and ecodynamics of enrichment culture facilities such as floating reefs and net cages.