The invention relates to a method for extracting oil by utilizing indigenous microbes of an oil pool subjected to polymer flooding. In the method, a method activating the indigenous microbes of the oil pool is adopted, and an activating agent comprises diammonium phosphate, sodium nitrate, molasses or cane sugar, compound amino acid, ammonium molybdate, copper sulfate, ferric chloride and zinc sulfate; and plugging can be further carried out on a deep channel and a roaring channel of the oil pool by injecting controlled-release nutritional agents and inorganic gel slugs. The method for extracting oil by utilizing the indigenous microbes of the oil pool subjected to the polymer flooding has obvious extraction rate enhancement effect, relatively low-cost used raw material and ground and underground dual environmental protection without increasing the difficulty of the post processing of produced fluids.