A three-dimensional hydrodynamic and sediment numerical model was used to simulate and analyze the local three-dimensional hydrodynamic characteristics and erosion-deposition characteristics of permeable double spur dikes with different opening rates and arrangement spacings, as well as their effects on aquatic habitats. The results show that the flow field structure around the permeable double spur dike is rich, forming the inner circulation of the upper spur dike, the main and auxiliary circulation between the dams and the slow flow area behind the lower spur dike, which is conducive to the enrichment of organic matter. When the opening rate is 15 %, the main circulation area and inter-dam vorticity of the pemeable double spur dike are the largest. The vorticity and turbulent kinetic energy near the dam increase with the increase of the arrangement spacing. Controlling the opening rate and appropriately increasing the arrangement spacing are beneficial to the migration of benthic organisms. The ratio of the maximum shear stress to the upstream shear stress gradually decreases with the increase of the opening rate and the arrangement spacing. Appropriately increasing the arrangement spacing and selecting a larger opening rate can reduce the scour of the discharged water on the riverbed behind the dam. The range and height of siltation in the dam and behind the dam decrease with the increase of the opening rate, and increase with the increase of the arrangement spacing. In the actual project, properly increasing the opening rate and the arrangement spacing can better achieve the effect of deceleration and siltation of the permeable spur dike, and provide abundant bait for benthic organisms.