BACKGROUND: Due to the rapid development of shale gas extraction, the treatment of flowback water (FW) is becoming one major challenge because of its high saline, high ammonium (NH 4 +), high phosphorus (PO 4 3−), and complex organic contents. This study aimed to treat the high-salinity synthetic FW and recover nutrient using the air-cathode (PMo/CB) microbial desalination cells (MDCs). RESULTS: The removal efficiency of chemical oxygen demand (COD) exceeded 90% along with an electricity generation of 105.6 mW m −2. The highest removal and the recovery efficiency of 300 mg L −1 NH 4 + and 100 mg L −1 PO 4 3− were 65.6 ± 19.0% and 75.8 ± 32.0%, 52.6% and 57.8%, respectively. High-throughput sequencing analysis of anodic biofilms indicated that Firmicutes, Bacteroidetes, and Proteobacteria enriched at high influent NH 4 + concentration were responsible for producing electricity and degrading complex organics. Two denitrifying bacteria, Trichococcus and Marinobacterium, promoted the COD removal and also improved the electricity generation. Rhodococcus, a kind of heterotrophic nitrification-denitrification bacteria, contributed to nitrification in the cathodic chamber along with enhancing the denitrifying degradation of COD. Nitrincolaceae, capable of heterotrophic nitrate reduction to ammonium, were favorable to the recovery of NH 4 +. CONCLUSIONS: Overall results concluded that PMo/CB-MDC could be a promising alternative technique for the efficient treatment of FW and a pretreatment process for separating nutrient from the recovery chamber.