Photocatalytic fuel cells (PFCs) are an energy-sustainable system concentrating on the degradation of refractory pollutants; however, their degradation efficiency still needs to be improved. Herein, a three-chamber photocatalytic fuel cell (PFC) was constructed based on the in situ utilization of junction potential created by a salt concentration gradient across the ion exchange membrane (IEM) for better degradation of rhodamine B (RhB). The system displays degradation efficiency as a linear function of NaCl concentration (y = 4.3089 × 10⁻⁴x + 0.0312, R² = 99.58%), with a maximum first-order kinetic constant (k) of 0.0505 min⁻¹ at a NaCl concentration of 45 g L⁻¹. In addition, the maximum power density increased rapidly from 170.00 to 319.70 mW m⁻² with an increase in NaCl concentration. Moreover, the salt solution was reduced in salinity by 19.70%, 41.69%, and 58.25% under an operation time of 12 h, 24 h, and 36 h. Furthermore, the photoanode exhibited greater degradation performance over time, which ensured the stable operation of the system. These results show that integrating salinity gradient power into the PFC system is an effective method to accelerate the degradation of refractory pollutants and to achieve the additional function of salinity removal.