To enhance urban surface source pollution control and promote the practical application of bioretention facilities, we investigated the change patterns of typical roof rainfall runoff pollution and the pollutant removal performance of assembled high-level parterre in Changsha by online and manual monitoring methods, and explored the structural composition of microbial communities in the facility medium by Illumina high-throughput sequencing. The results showed that the concentrations of COD and SS in the initial roof rainfall runoff of Changsha were 22.9-153.0 mg/L and 58.4-294.4 mg/L, respectively, indicating that the initial runoff was highly polluted, and the COD and SS showed a trend of positive correlation. The peak concentration of pollutants occurred within 30 min after the start of rainfall and gradually decreased and stabilized with the increase of rainfall duration. The increase of rainfall volume, rainfall intensity and rainfall interval would aggravate the initial flush and further deteriorate the water quality of roof rainfall runoff. The removal rates of COD, SS and NH3—N in the assembled high-level parterre were 58.3%, 85.3% and 66.2% and above, respectively, and the water quality of the roof rainfall runoff was significantly improved after purification. The main dominant phyla in the medium of high-level parterre were Proteobacteria, Actinobacteria, Acidobacteria and Chloroflexi, among which the relative abundance of Proteobacteria accounted for 30.0%-46.6%. Furthermore, the denitrification process was more likely to occur at the effluent end.