Abstract: The invention discloses a method of isolating nucleic acid and the system thereof, which relates to the following process: (1) providing a biological sample containing cells; (2) performing a cell concentration procedure; (3) performing a magnetic separation procedure through a magnetic separation unit; (4) performing a suspension procedure through a suspending unit; (5) performing a lysis procedure through a lysis unit; and (6) performing a nucleic acid extraction procedure to extract the nucleic acids from the biological samples; wherein the cell concentration procedure does not involve any means of centrifugation. Therefore, the method is simple and efficient, and it is particularly favorable in full automation of nucleic acid isolation. Furthermore, the method and the system as a whole further include a clarification procedure executed by a clarification unit without using centrifugation means, so that improves the quality of nucleic acid isolation.