The invention discloses a method for determining low-concentration protein in secondary output water of a sewage plant, belonging to the field of municipal sewage treatment. The method comprises the following steps: preparing a reagent, establishing a mathematical model, pretreating a sample, determining the concentration of the protein and the like. Based on a Lowry method and an improved Lowery method, a Minitab response surface method is used for analyzing the content of the protein so that the problems of low accuracy and low precision of the determination of the protein in real sewage are overcome; and the interferences on humic acid, carbohydrates, and ions including Ca<2+>, Mg<2+> and the like in the secondary output water are reduced. The method for determining the low-concentration protein in the secondary output water of the sewage plant has the advantages of high accuracy, simplicity, easiness for operation and the like, is suitable for determining the low-concentration protein in the secondary output water of the sewage plant, and can be used for synchronously determining the concentration of the humic acid in the secondary output water, so that the applicable range is wide.