The invention provides a method for effectively extracting genomic DNA (deoxyribonucleic acid) of melaleuca alternifolia, which comprises the following steps: (1) grinding a sample into powder by liquid nitrogen, transferring the powder to a centrifuge tube, adding a DNA extraction buffer which is conventionally preheated, uniformly mixing and carrying out water bath at 65 DEG C for 30 minutes; (2) taking out the centrifuge tube and cooling to room temperature, adding a mixed solution of chloroform and isoamyl alcohol, uniformly mixing and performing centrifugal separation; (3) taking supernate, adding chloroform, uniformly mixing and performing centrifugal separation; (4) taking supernate, adding absolute ethyl alcohol which is conventionally precooled, uniformly mixing, standing for 30 minutes at -20 DEG C, then performing centrifugal separation, and discarding the supernate; (5) washing sedimentation with ethyl alcohol of which the volume concentration is 75%, drying at room temperature and adding a DNA dissolution buffer, and storing at -20 DEG C for standby use. The method provided by the invention is capable of effectively and rapidly extracting the genomic DNA of the melaleuca alternifolia which is high in purity and suitable for PCR detection, and the use of toxic chemicals in the extracting process is reduced.