The anaerobic biodegradation of polycyclic aromatic hydrocarbons (PAHs) in high salinity wastewater is rather hard due to the inhibition of microorganisms by complex and high dosage of salts. Microbial electrolysis cell (MEC), with its excellent characteristic of anodic biofilms, can be an effective way to enhance the PAHs biodegradation. This work evaluated the impact of NaCl concentrations (0g/L, 10g/L, 30g/L, and 60g/L) on naphthalene biodegradation and analyzed the damage protection mechanism of anodic biofilms in batching MECs. Compared with the open circuit, the degradation efficiency of naphthalene under the closed circuit with 10g/L NaCl concentration reached the maximum of 95.17% within 5days. Even when NaCl concentration reached 60g/L, the degradation efficiency only decreased by 10.02%, compared with the MEC without additional NaCl. Confocal scanning laser microscope (CSLM) proved the superiority of the biofilm states of MEC anode under high salinity in terms of thicker biofilms and higher proportion of live/dead bacteria cells. The highest dehydrogenase activity (DHA) was found in the MEC with 10g/L NaCl concentration. Moreover, microbial diversity analysis demonstrated the classical electroactive microorganisms Geobacter and Pseudomonas were found on the anodic biofilms of MECs, which have both PAHs degradability and the electrochemical activity. Therefore, this study proved that high salinity had adverse effects on the anodic biofilms, but MEC alleviated the damage caused by high salinity.