Plasma advanced oxidation process (PAOP) has great ability to break recalcitrant pollutants into small molecular compounds but suffers from poor performance and low energy efficiency for mineralizing dyeing pollutants. Combining advanced oxidation process with biodegradation process is an effective strategy to improve mineralization performance and reduce cost. In this study, a combined process using PAOP as pre-treatment followed by microbial fuel cell (MFC) treatment was investigated to mineralize methylene blue (MB). The PAOP could degrade MB by 97.7%, but only mineralize MB by 23.2% under the discharge power of 35 W for 10 min. Besides, BOD5/COD ratio of MB solution raised from 0.04 to 0.38 while inhibition on E. coli growth decreased from 85.5% to 28.3%. The following MFC process increased MB mineralization percentage to 63.0% with a maximum output power density of 519 mW m-2. The combined process achieved a mineralization energy consumption of 0.143 KWh gTOC-1 which was only 41.8% of that of PAOP. FT-IR, UV-vis and pH variation demonstrated that PAOP could break the aromatic and heterocyclic structures in MB molecule to form organic acids. Possible degradation pathways of MB were accordingly proposed based on LC-MS, GC-MS, and density functional theory calculation.