Recently, the endocrine-disrupting and carcinogenic compound di-(2-ethylhexyl) phthalate (DEHP) has gained increased attention. In this study, the enhanced effect of cometabolism on DEHP removal and the associated microbial processes in an extended granular sludge bed (EGSB) reactor over 293 days were investigated. The results indicated that it took 181 days to start up the reactor, with only a 38.5% removal efficiency when treating 0.6 mg/L DEHP wastewater. The addition of glucose at low concentrations (1 and 2 g/L) promoted DEHP removal. However, higher concentrations (5 and 10 g/L) inhibited the bioprocess. In contrast, yeast enhanced DEHP degradation at all of the tested concentrations (0.1, 0.2, 0.3, and 0.4 g/L). Quantitative real-time PCR (q-PCR) and statistical analysis demonstrated that the amount of the archaea and DEHP removal were positively correlated (r = 0.99, p < 0.05). A MiSeq sequencing analysis revealed that the microbial community had an obvious shift that accompanied the increasing DEHP removal rate. Bacteroidetes and Firmicutes maintained a relatively constant abundance during the entire trial, while Spirochetes and d-Proteobacteria gradually became predominate in the EGSB reactor. At the genus level, the relative abundance of Levilinea, Thauera, and Actinobaculum gradually decreased. For the archaea, the acetoclastic methanogens, Methanosaeta and Methanosarcina, existed in the EGSB reactor throughout the experiment. This study suggests that cometabolism is feasible for enhancing DEHP wastewater treatment, and it shows the potential for practical applications in engineering.