The release of printing and dyeing wastewater (PDW) into the environment is a concern attributed to its acute, chronic and cytotoxic effects to aquatic life. Two anaerobic/aerobic-membrane bioreactors (A/O–MBRs) were operated continuously to treat raw (untreated) and Fenton oxidized PDW. After about 70 days acclimatization, 67% of the chemical oxygen demand (COD) and 35% of adsorbable organic halogens (AOX) were removed by direct biodegradation in A/O–MBR without Fenton pre-treatment, while 90% of the COD and 79% of AOX were removed in Fenton + A/O–MBR system. Fenton oxidation play a dominate role on the COD and AOX removal of PDW in the combination system. The Fenton pre–treatment of PDW could remarkably reduce membrane fouling. The Shannon indices showed that the microbial diversity in anaerobic flocs were significantly higher than the microbial diversity in aerobic flocs in both two A/O–MBR systems. The metagenomics analysis found that the key functional genes responsible for the AOX biodegradation were EC3.1.1.45, pcaI, and pcpD. The transcript per million (TPM) abundance of EC3.1.1.45 and pcaI significantly up-regulated in both anaerobic and aerobic flocs after 70 days acclimatization. Based on the pilot applications study, the total operation cost of Fenton + A/O–MBR processes for PDW remediation was approximately 1.263–1.384 USD/t. This study provides a promising technique for removing AOX and other organic contaminants from PDW.