Mixed pharmaceutical wastewater contains high levels of chemical oxygen demand (COD) and high concentrations of toxic and harmful substances. A conventional wastewater treatment process cannot treat this wastewater sufficiently to meet discharge standards. Therefore, mixed pharmaceutical wastewater treatment is a serious challenge to wastewater management. In this study, a full-scale combined anaerobic/ oxic (A/O) and biological filtration oxygenated reactor (BIOFOR®) process was used to treat the mixed pharmaceutical wastewater. The objectives were to evaluate the removal efficiency of the combined A/O+BIOFOR process on mixed pharmaceutical wastewater and to examine the bacterial community structures in process. The results showed that the effluent concentration of COD, NH₄^--N, and SS could meet the Chinese mission standard of water pollutants for the pharmaceutical industry mixing/compounding and formulation category (GB21908-2008). MiSeq sequencing data showed that the two systems (A/O and BIOFOR) harbored different bacterial diversity and communities. In phylum level, candidate-division-TM7 was the most predominant phylum in the A/O system, while Proteo bacteria was the most dominant phylum in the BIOFOR reactor. At the genus level, 126 genera were unique in A/O or BIOFOR reactors. The results of this study provided insights into the bacterial community structure and diversity in pharmaceutical wastewater treatment system and can provide reference for the treatment of mixed pharmaceutical wastewater.