The invention belongs to the technical field of molecular biology, and discloses an extraction method of microorganism genome DNA. The extraction method comprises the following steps: (1) collecting sample thallus, adding a STES buffer solution, re-suspending, adding glass beads, and dissolving by virtue of a TE buffer solution; (2) adding an equal volume of phenol/chloroform solution, oscillating, mixing, and primarily centrifuging; (3) adding an equal volume of chloroform/isoamylol solution into an upper layer of water after the primary centrifuging, mixing, and secondarily centrifuging; (4) adding an equal volume of isopropanol or twice volume of anhydrous ethanol into an upper layer of water after the secondary centrifuging, precipitating under the room temperature, tertiarily centrifuging, and collecting precipitates; (5) washing the precipitates by utilizing ethanol, re-centrifuging to obtain DNA precipitates, dissolving the DNA precipitates by utilizing sterile water, carrying out the magnetic-ball passivation, to obtain extracted microorganism genome DNA. The genome DNA obtained by virtue of the method has advantages of high concentration, single banding and no pollution, and satisfies the three-generation sequencing requirement.