Disclosed is a disk based system for separating at least two types of particulates contained in a sample fluid. The system includes a disk-like carrier board and a magnetic attraction unit. The disk-like carrier board forms at least one flow channel structure, which includes an inner reservoir, at least one separation chamber, and at least one outer reservoir arranged in sequence from a geometric center of the disk-like carrier board to an outer circumferential rim of the disk-like carrier board. A method of separation carried out with the system includes introducing the sample fluid into the inner reservoir and then rotating the disk-like carrier board to induce a centrifugal force. The sample fluid contains particulates that are labeled with immunomagnetic beads and the labeled particulates are attracted by the magnetic force generated by the magnetic attraction unit to retain in the inner reservoir or the separation chamber. Particulates not labeled with the immunomagnetic beads and contained in the sample fluid move with the sample fluid to the outer reservoir.