A better understanding of the alteration of organic pollutants and microorganisms in wastewater biotreatment processes is essential for the elucidation of pollutant removal mechanisms. This study investigated the alteration of organic pollutants, microbial communities and functional genes in a petrochemical wastewater treatment plant in China. Results show that the dominant organic components are phenols and aromatic amines in the influent of the biotreatment process, while linear hydrocarbons remained in the effluent. Microorganisms in the activated sludge samples were mainly bacteria, with Rhodocyclales and Burkholderiales dominating in the biotreatment process, but their relative abundances decreased dramatically during the biotreatment process, along with the removal of organic compounds. Based on functional gene annotations from the eggNOG database, the microbial community possessed high numbers of genes associated with amino acid transport and metabolism, energy production and conversion, replication, recombination and repair, and cell wall/membrane/envelope biogenesis. Generally, the relative abundances of KEGG orthologous genes involved in alkane and aromatic degradation initially increased, then dropped during the biotreatment process. This study gives insights into the mechanisms of petrochemical biodegradation processes in wastewater treatment plants.