Phenol, which is a typical recalcitrant refractory organic poses a severe hazard to ecosystems even at low concentrations. Although numerous bio-approaches have been dedicated to eliminate the contamination coupling with denitrifying, the interactive mechanism and relationship remain poorly understood. In this study, a strain identified as Burkholderia PHL5 with efficient phenol degrade capacity was isolated from activated sludge. During the degradation process, most of the phenol (44.36%) was mineralized, while 36.79% phenol was assimilated by the strain and only 18.85% phenol was degraded to long-chain organic compounds. Also, phenol degradation was accompanied by the formation of catechol, mediated by the multicomponent phenol hydroxylase (LmPH) initially, which could be corroborated by the amplification of the functional LmPH gene. Two vital long-chain organics intermediates, namely, bis(6-ethyl-3-octanyl) oxalate and 6-ethyl-3-octanyl 4-methylpentyl oxalate, were identified in the degradation process, indicating that phenol underwent meta-ring opening cleavage pathway mediated by the strain. Moreover, the biodegradation of phenol by the strain was found to be an N-dependent process, whereas the nitrate could exacerbate the phenol degradation rather than acting exclusively as the electron acceptor and nitrogen source. Lastly, a positive relationship of initial phenol concentration and phenol vs. nitrate ratio on phenol degradation was discerned. Overall, these findings deepened the understanding of recalcitrant refractory organic degradation, thereby providing an eco-friendly strategy for the decontamination of the targeted contaminant in an application.