The invention provides a method for marking protein by a carboxyl microsphere, belonging to the field of preparation of immunologic diagnosis kits. According to invention, in a system for marking the protein by the carboxyl microsphere, according to the content of carboxyls on the surface of the microsphere, the molar ratio of cross-linking agents EDC to -COOH is set to be (0.8-2) to 1, and the molar ratio of EDC to NHS or Sulfo to NHS is (1-3) to 1, so that the optimal ratio of the number of the carboxyls on the surface of the microsphere to the number of activated carboxyls is achieved; meanwhile, the pH is regulated, so that the reaction system is rapidly converted from condition beneficial for activation into state beneficial for antibody connection, the step of centrifugalization or tangential flow filtering is saved, and finally, the purposes of simplifying marking steps, saving cost, and marking protein by the carboxyl microsphere efficiently are achieved. The method provided by the invention can be applied to preparation of a detection kit taking the latex microsphere or the magnetic microsphere as a carrier, and has good market application prospect and economic value.