Hydraulic fracturing wastewater (HFW), a byproduct of hydraulic fracturing oil extraction, contains a complex mixture of oil, aldehydes, and benzene compounds. Efficient and eco-friendly HFW treatment means are critical for the oil extraction industry, particularly in developing countries. In this study, two biological processes namely an anaerobic/anoxic/moving bed biofilm reactor (A-MBBR) and an A-MBBR with a microfiltration membrane (A-MFMBBR) were established, and assessed for the real HFW treatment. Removal efficiencies of chemical oxygen demand (COD) and NH-N were over 92% and 95%, respectively, in both processes with a hydraulic retention time of 72 h. The majority of organic compounds in both systems identified by GC–MS were degraded in the anaerobic units. In comparison, A-MFMBBR demonstrated higher removal efficiencies for oil, total suspended solids, and complex compounds. The average relative abundances of refractory compound degrading bacteria were 43.4% and 51.6% in the A-MBBR and A-MFMBBR, respectively, which was consistent with the COD and oil removal, and suggested that the MBR could maintain a high diversity of microorganisms and contribute to deep recalcitrant organics degradation. This study sheds light on the potential of using a compact biological process for the real HFW treatment.