The invention discloses a method for separating free nucleic acids from a sample containing free nucleic acids, wherein the method includes the steps: adding protease K and a lysis-binding solution to a test sample, after centrifugation, adding alcohols and making contact with a solid carrier, making the free nucleic acids in the sample bind to the solid carrier, and then washing the solid carrier with one or more washing solutions; and finally, adding an eluant to the solid carrier, to obtain the target product free nucleic acids, wherein the pH of the lysis-binding solution is acidic, and all the steps are carried out at room temperature. The invention also discloses a system for separating the free nucleic acids, wherein the system includes the lysis-binding solution, the washing solution, the eluant, a liquid storage tube, a nucleic acid purification column tube, and a vacuum adapter tube. The method and system for separating the free nucleic acids have the advantages of simple operation, low cost, wide applicability, high yield, and reliable purity, and has wide application value and good market prospect.