The invention discloses a separate detection system and method of rare cells based on a centrifugal micro-fluidic technology. The system comprises a micro-fluidic chip similar to an optical disk, a centrifugal drive module and an optical detection module, wherein the micro-fluidic chip comprises a plurality of groups of micro-channels and micro-cavities arranged in a radiation manner; and the entire chip structure is composed of an elastic micro-column guide rail layer, a deformable film layer, a pipeline/cavity layer, a filtering membrane layer and a liquid waste collecting layer. The method comprises the steps of: firstly, leading a sample solution and immune modified microspheres into a liquid storage cavity through an injection port of the micro-fluidic chip in use, putting the sample solution and the immune modified microspheres on a centrifugal platform of the centrifugal drive module, assembling an elastic micro-column, and rotating at a low speed, so as to achieve fully mixing and reacting of the sample solution and immune modified microsphere liquid in the liquid storage cavity, separating by a high-speed rotary chip, and then dropwise adding a specifically recognized fluorescently-labeled antibody solution in each separate cell collection area, carrying out incubate reaction, adding a buffer solution and centrifuging, and finally identifying and analyzing through the optical detection module.