Abstract: A multidimensional liquid chromatography separation system has a mobile-phase storage tank, a first liquid transfer device, a second liquid transfer device, a first sample introduction device, a second sample introduction device, a separation device, a collection, storage device, at least two drainage devices and a flow path switching device. A separation method for protein separation using the multidimensional liquid chromatography separation system has the steps of: 1) preparation in advance, 2) the first dimensional separation, 3) collection and storage of the intermediate fraction, 4) the second dimensional or multidimensional separation and repeating the steps 3) and 4).