The invention discloses a column chromatography isolation fully-automatic part collection device and method. The a column chromatography isolation fully-automatic part collection device comprises a bottom plate; a test tube plate is arranged above the bottom plate; a test tube rack is arranged above the test tube plate; and a waste liquid tank is arranged on the left side of the test tube rack. The bottom plate is perpendicularly connected with a box body; an X-axis slideway is arranged in the box body; the X-axis slideway is perpendicularly connected with a U-axis suspending arm; a Y-axis slideway is arranged on the right side of the Y-axis suspending arm; the Y-axis slideway is connected with an electromagnetic timing switch; a three-way valve is arranged above the left back of the box body; and a three-way valve input end, an effective liquid output pipe orifice and a waste liquid output pipe orifice are formed in the three-way valve. By adoption of square design and a suspending type X-Y moveable moving mode, pipe change is precise in positioning; and the collected solution is separated from the circuit, so that the device is safer to use. Through the three-way valve and the control program, the waste liquid automatically flows into the waste liquid tank. Through electromagnetic valve control, a liquid leakage phenomenon in the pipe changing switching process is avoided. The device can replace manual collection of samples, is simple and convenient to operate, improves the working quality and efficiency, and reduces harm on experimenters by organic solvents.