In order to study the distribution, amplification and correlation of microbial community structure and resistance genes in pharmaceutical wastewater, a variety of biological treatment processes are used to treat pharmaceutical wastewater. Combining Miseq high throughput sequencing analysis technology and fluorescence quantitative PCR technology, activated sludge in pharmaceutical wastewater plants is detected. The results show that sul1, sul2, tetO, tetQ, tetW, OXA-1 and INT1 are widely detected at all stages of pharmaceutical wastewater treatment plant. The total resistance gene concentration ranges from 3.09×10⁸ to 2.26×10⁹ copies/g (dry weight), and the total gene concentration increases by 7.3 times. Miseq sequencing results show that the dominant bacteria in pharmaceutical wastewater are Proteobacteria, Bacteroidetes, Firmicutes, Thermus and Gemmatimonadetes, with an average relative abundance ratio of 81.05%. Redundancy analysis shows that Aeromicrobium is positively correlated with sul2 to a high degree, which might be sul2 existing in microbial communities. Among the possible major microflora, Rhodovulum and Rhodospirillaceae are highly positively correlated with OXA-1 and tetQ, which are the main microflora of ARGs distribution. Acinetobacter has a high degree of positive correlation with tetO and tetW, which may be the main possible microflora of tetO and tetW in microbial community. The results show that appreciation and distribution of antibiotic resistance gens are connected with concerned specific bacterial genus. The controlled abundance of concerned bacterial genus could subduce resistance gene in industrial wastewater factory.