The current study was aimed to investigate the filler layer structure in modified bioretention systems. Three different structural layers in bioretention were proposed to evaluate their hydrologic performance and pollutant removal efficiency under different rainfall intensities. These layers were as follows: all three layers (filter, transition, and drainage layers), without transition layer, and without drainage layer. Synthetic stormwater was used for experimental purpose in current work. Results revealed that compared with “all three layers”, runoff control rate of “without transition layer” and “without drainage layer” was reduced by 0 to 7.4%, 0 to 10.1%, and outflow start time was advanced by 6 to 8 min and 1.5 to 4.5 min, respectively. Moreover, CODcr (chemical oxygen demand), NH4+-N (ammonium nitrogen), TN (total nitrogen) and TP (total phosphorus) removal rates were 86.0%, 85.4%, 71.8%, and 68.0%, respectively. Particle size distribution of the fillers revealed that during operation, particle moved downward were mainly within 0.16–0.63 mm size. Findings showed that transition and drainage layer played an important role in runoff control, and total height of the filler layer should not be less than 800 mm. Filter layer effectively reduce runoff pollution but the thickness of the filter layer should not be less than 500 mm. Whereas, transition layer has the function of preventing the filler loss of the filter layer; therefore, proper measures must be taken into consideration during structural optimization.