The invention relates to a removing method for nitrate in a micro-polluted water body and belongs to the field of wastewater treatment. The method comprises the steps that a certain amount of herba houttuyniae, herba incarvller and kudzu are taken and smashed, absolute ethyl alcohol is added, the mixture passes through a chromatographic column, and a mixture composed of chlorophyll a and bacteriochlorophyll is extracted; the mixture is placed into a colorimetric tube with a plug, protein and pectin are added and mixed with the mixture to be even, titration is performed through diethyl ether, and filtration is performed through a filter membrane for sterilization; sodium dihydrogen phosphate and magnesium chloride are dissolved in de-ionized water, and after being stirred and cooled, the solution is added into the chlorophyll a and bacteriochlorophyll mixed liquid sterilized through the filter membrane; succinic acid is added to adjust pH; methanol and ethyl acetate are added into the mixed liquid and stirred, in addition, glutamic acid is added, sterilization is performed, pH is adjusted, cooling is performed, and sterile filtration is performed to obtain colorless supernatant liquid; a sodium thiosulfate solution and a magnesium chloride solution are added into the supernatant liquid, pH is adjusted, and the mixed liquid is cooled, sterilized, mixed and then poured into a sterilized test tube for low-temperature storage out of the sun. Equipment is low in manufacturing cost, running costs are low, and management is easy and convenient; besides, phosphate removal is efficient, low in consumption and free of secondary pollution.