The water body inside the constructed wetland is affected by various factors, and the flow state is relatively complicated. There will always be a certain degree of low velocity area and rapid outflow phenomenon, which makes part of the space in the wetland unable to be effectively used. Based on Computational Fluid Dynamics (CFD) technology, this paper uses Fluent's porous media model and discrete phase model to establish a hydrodynamic model of up and down baffled subsurface flow constructed wetland system. The internal flow field of the wetland is simulated, and the hydraulic performance of different baffle settings and substrate laying methods in the wetland is systematically evaluated. The results show that when the number of baffles is the same, the hydraulic efficiency is higher when the first baffle is located on the lower part of the substrate. Compared with the position of the baffle, the increase in the number of baffles does not significantly improve the hydraulic efficiency of the constructed wetland. The substrate layer thickness ratio has a significant effect on the two parameters of the variance of the hydraulic residence time distribution (σ2) and the flow divergence (σ02). By increasing the thickness of the middle substrate, the low flow rate phenomenon caused by the small porosity substrate area of the upper layer and the rapid outflow phenomenon of the lower substrate can be improved to a certain extent, the utilization efficiency of the middle substrate layer is improved, and the hydraulic performance is increased. The research results are of great significance for improving the utilization of wetland space and ensuring its efficient decontamination and purification function.