The invention relates to a method for separating free nucleic acid from a blood serum or blood plasma sample by using a magnetic bead, and belongs to the field of nucleic acid purification. The method comprises the following steps: firstly adding the blood serum/blood plasma sample, a lysis buffer, protease K and magnetic bead suspension liquid into a nuclease-free centrifugal tube, fully and uniformly mixing, then performing pyrolysis, adsorbing nucleic acid on the surface of the magnetic bead, performing purification under the effect of an external magnetic field, removing impurities such as protein, polysaccharide, salt and the like through a rinsing step, and finally eluting by adding nuclease-free water to obtain a free nucleic acid solution. The method disclosed by the invention has the characteristics of simplicity, high speed, stability, high efficiency and cheap price; the purified free nucleic acid is complete and high in purity, and can be directly used for subsequent experiments.