The migration and transformation model was established to represent organic pollutant flow patterns in a subsurface flow wetland (SSFW). In order to simulate internal flow field and water quality concentration in a wetland system simultaneously, the porous media model coupled with a Monod equation were introduced to describe hydraulic characteristics and biodegradation. The parameters of the model were tested and verified by a series of experiments. The result showed that this model could reasonably simulate organic pollutant removal in SSFW. Theoretically, a backwater zone and rapid channel would appear in SSFW of different substrate filler, which could influence hydraulic efficiency and pollutant removal effects. Seven kinds of typical organic pollutants were selected, and the ranking of their removal efficiency was in the order of aminobenzene, phenol, dimethylbenzene, toluene, benzene, nitrobenzene, and chlorobenzene. The treatment effects of select control organic pollutants could be improved by extending the retention time and increasing adsorption quantity through further filler optimization.