An automated continuous purification system includes a base and a plurality of purifying elements. The base includes a first flowing channel layer, a rotation valve, a plurality of second flowing channel layers, a plurality of third flowing channel layers and a top layer, which are overlapped from bottom to top, and the second flowing channel layers are overlapped correspondingly with the third flowing channel layers. Inlets of the top layer is connected with outlets of the top layer through first flowing channels of the first flowing channel layer, through holes of the rotation valve, second flowing channels of the second flowing channel layers and third flowing channels of the third flowing channel layers, and the outlets are further connected with the purifying elements by pipes. The rotation valve can be driven and rotated by a first force so as to make each of the through holes be connected with another second flowing channel. Therefore, the automated continuous purification system can perform continuous purification process. |