The invention provides a pharmaceutical wastewater treating system, and relates to the field of environmental protection. The pharmaceutical wastewater treating system comprises a mixing tank, a settling tank, a multi-stage electrolytic tank, a multi-stage Fenton phase tank, a first heater, a first evaporator, a second heater, a second evaporator, a third heater, a third evaporator, a gas-liquid separator and an intermediate tank. The mixing tank is communicated with the settling tank, the multi-stage electrolytic tank is connected with the multi-stage Fenton phase tank, the multi-stage Fenton phase tank is connected with the first heater, the first evaporator is communicated with the second heater, the second evaporator is communicated with the third heater, the third evaporator is connected with the gas-liquid separator, the intermediate tank is connected with the multi-stage Fenton phase tank, and the intermediate tank is connected with a third circulation pipe through a vacuum pipe. The pharmaceutical wastewater treating system is high in waste treatment efficiency, the pollution index of treated waste water is greatly reduced, and the content of organics and the content of hazardous substance are obviously reduced. The invention further provides a treating method.