The traditional bioretention systems possess a remarkably low nitrogen and phosphorus removal effect. The removal rate fluctuates greatly, and even appears as negative removal of nitrogen and phosphorus. The four simulated bioretention experimental columns with different bilayer media, packing composition and structure were constructed. Based on the traditional fillers, the modified composite fillers with hydroxy-aluminum and modified vermiculite sludge particle (HAVSP) were added. The traditional filler (C1) and the modified composite filler (C2) were added respectively, moreover the saturated zones were set up to enhance the effect of nitrogen and phosphorus removal. Removal of nutrients from experimental columns by simulated runoff efficiency was evaluated and compared. In addition, the effect of media depth on phosphorus retention and denitrifying enzyme activity in bioretention columns was also evaluated. The experimental column #2 filled with C2 had the optimum removal effect on total phosphorus (93.70%), however, the removal effect of total phosphorus by filling C1 experimental columns was insufficient (57.36%). Designed to remove nitrate (NO3−-N) and total nitrogen (TN), the experimental column #4 showed the best performance (83.54% and 92.15%, respectively). In this study, we propose a fold-flow bioretention system by filling HAVSP in combination with saturated zones. The runoff water quality can be effectively improved, and a new bioretention cell configuration can be provided for efficient stormwater treatment.