The present invention provides an electromagnetic stirring separation device for biopharmacy. The device includes an operation surface, a body, a stirring base and a support bar. The outer surface of the operation surface comprises a display screen, a switch and an automatic switch; a support plate is fixedly mounted on the upper end face of the body; the body is internally provided with a cavity; the cavity is internally provided with a control unit, a variable-frequency power source and a sensor; and the control unit includes a printed circuit board and an A / D converter welded to the printed circuit board, an embedded central processing unit, a storage, a D / A converter, a relay and a battery. Compared with the prior art, the device provided by the present invention has the following beneficial effects: the device prevents inadvertent tough of switch by the staff in case of an accident leading to accidental opening of the device, so as to enhance the use safety; the device can be automatically controlled, and has the advantages of minimal impact on the pharmaceutically activity, high separation efficiency, easiness to use and operation, good stability and high reliability.