The invention discloses a high salinity pharmaceutical wastewater processing system, wherein the salinity tolerance range of the system of the invention is that the total salinity is less than 5%, and is generally less than 3%. The system which adopts a processing technology with "a catalytic micro-electrolysis device, a hydrogen peroxide catalytic oxidation tank, a photosynthetic bacterium anaerobic system, a photosynthetic bacterium aerobic system and a coagulation decoloring tank" allows COD, BOD, ammonia nitrogen, and the chroma to be furthest reduced, the processing effect to be uninfluenced by the salinity, and outlet water to reach discharge standards. The system which allows various high salinity pharmaceutical wastewaters to be effectively processed, abuses of dilution or evaporation (burning) processing technologies for the routine processing to be avoided and the total pollutant discharge amount to be reduced and has the advantages of strong operation stability, low investment cost, high processing efficiency and low operation cost is a high salinity pharmaceutical wastewater processing system with development potential.