Abstract: The coking wastewater with high concentration organic matter was treated by a two-stage anoxic/oxic (A/O) process to explore the relationship between the transformation of organic pollutants and bacterial community structure. Fourier transform infrared spectroscopy and three-dimensional fluorescence spectroscopy were used to analyze the functional groups of organic pollutants and dissolved organic matter in this two-stage A/O process. The structure and function of the microbial ecosystem were explored using high-throughput sequencing technology. The results showed the two-stage A/O process removed more than 90% of chemical oxygen demand from ammonia-borne nitrogen, thiocyanate, benzoapyrene, phenol, and volatile phenols. The removal of each organic pollutant is related to shift in stretching vibrations of functional groups such as C≡N, C—N, C=C and —CO—, and bending vibrations of C—N and N—H. Such changes are applicable to alcohols, lipids, ethers, polysaccharides, and carboxylic acids. Additionally, most of DOM was removed from the original water. Microbial analysis showed Thiobacillus to be the dominant genus over the course of the treatment process (relative abundance ranging from 18.85% to 31.06%). Relative abundance of Fluviicola and Norank_F_JG30-KF-CM45 were negatively correlated with BaP concentration, while relative abundance of Arenimonas were positively correlated with the concentration of volatile phenol and phenol. Relative abundance of Bradyrhizobium, Nakamurella, Nitrospira, norank_f_NS9_marine_group and unclassified_f_Rhizobiaceae were negatively correlated with the concentration of volatile phenol and phenol. Furthermore, PICRUSt2 functional prediction analysis showed the removal of organic pollutants was associated with various metabolic pathways, such as the degradations of fluorobenzoate, PAH, and benzoate. The study showed that the main pollutants in coking wastewater were significantly removed by two-stage A/O process, and the change of organic pollutants affected the change of the relative abundance of functional microorganisms