This study assesses the use of vertical greening for blackwater treatment. The effects of hydraulic retention time (HRT) and drip frequency on treatment performance were systematically studied. Additionally, microbial communities in the vertical greening system were characterized. The results show that the removal efficiencies of NH4+-N and total phosphate (TP) increased with an increase in HRT, and the drip frequency had a significant effect on TP. High-throughput sequencing revealed that the diversity of the microbial community did not change significantly along vertical and horizontal directions, but the dominant species shifted. Heterotrophic nitrifying and denitrifying bacteria decreased significantly while autotrophic nitrifying bacteria, especially ammonia oxidizing bacteria, proliferated in a vertical direction. Therefore, it is concluded that vertical greening systems can effectively treat blackwater and lower NH+-N levels.