The invention discloses a DNA extraction method suitable for structural analysis of microbial community in sediment, which comprises the following steps: washing a sediment sample with TENPbuffer, and suspending the washed sediment sample in PBS buffer; repeatedly freezing and melting the pretreated sediment sample, adding muramidase, adding proteinase K and sodium dodecyl sulfate into the sediment sample, centrifuging the sample at room temperature, taking supernate, adding mixed solution of phenol, chloroform and isoamylol in equal volume into the supernate, mixing evenly by oscillation, centrifuging the obtained sample at room temperature, taking a liquid phase, adding mixed solution of chloroform and isoamylol in equal volume into the liquid phase, centrifuging the obtained sample at room temperature, taking a liquid phase, and adding precooled isopropanol into the liquid phase; centrifuging the obtained sample to remove supernate, adding precooled ethanol into the sediment, washing the sediment for three times, and centrifuging to remove the ethanol; and naturally air-drying the sample, and dissolving DNA with TE buffer solution for preservation.