In this study, the synergistic effects and mechanisms of biodegradation on aromatic compounds including phenol (PHN), naphthalene (NAP), phenanthrene (PHE), and pyrene (PYR), respectively as the only carbon source by bacterial flora were investigated. The results indicated that the bacterial flora showed good synergistic effects for the degradation of aromatic compounds. The removal rate of TOC, compared with the single strain, was improved by 9.85%, 11.57% and 12.41%, respectively, for the degradation of NAP, PHE, and PYR, and their toxicity reduction was also significantly improved. Synergistic mechanisms of bacterial flora on aromatics biodegradation indicated that the diversity of bacterial flora increased with the increase of molecular weight of aromatic compounds, and the coordinated metabolic activities of bacterial flora significantly enhanced its activity. Highly active microorganisms promoted the secretion of EPS, and the contents of EPS were positively related to the molecular weight of aromatic compounds, which would enhance the resistance of microorganisms to toxic environment and the bioavailability of polycyclic substances. In addition, the expression time of C23O activity was advanced by 6 h and the activity was also increased by 1.23–1.70 times under the synergistic effect of the bacterial flora, and the activity showed different responses due to different structures of aromatic compounds.