The invention relates to a pharmaceutical wastewater advanced treatment system. The pharmaceutical wastewater advanced treatment system comprises a wastewater regulating tank, a coagulative precipitation tank, an ozone oxidation floatation tank, a packed-type anoxic / anaerobic reaction tank, an aerobiotic contact oxidation tank, a secondary sedimentation tank, an electrolytic tank, a countercurrent type biological aerated filter and a clear water tank, wherein the coagulative precipitation tank comprises a stirring mixing zone and a precipitation zone, the ozone oxidation floatation tank comprises a mixing zone and a separation zone, the packed-type anoxic / anaerobic reaction tank is divided into a facultative anaerobic section, an anoxic section and an anaerobic section by baffle plates, the aerobiotic contact oxidation tank is provided with a water inlet pipe and a water distribution triangle pyramid, an aeration regulation control system is arranged at the lower part of the water distribution triangle pyramid and comprises an aeration tray, an air blower and a dissolved oxygen measurement regulation control device, the electrolytic tank is divided into a left compartment and a right compartment which are respectively a positive electrode compartment and a negative electrode compartment, the bottoms of the positive electrode compartment and the negative electrode compartment are communicated, the middle upper parts of the positive electrode compartment and the negative electrode compartment are separated by baffles, and the positive electrode compartment and the negative electrode compartment are respectively provided with a positive electrode plate and a negative electrode plate, and the countercurrent type biological aerated filter comprises a downstream zone, an upstream zone and a sludge zone.