The invention discloses a method of detecting the residue of small-molecule substances harmful to the human body and a special kit. The special kit comprises a non-transparent micro-porous plate and a light-emitting compound, wherein each hole of the non-transparent micro-porous plate is filled with a coat antigen which is simultaneously coated with three kinds of small-molecule substances. The invention makes full use of the multi-color marking function of QDs, establishes a novel kit for simple and rapid detection of the residue and a method thereof, and realizes the multi-color marking through indirect marking of polyclonal antibodies and monoclonal antibodies in the veterinary drug by coupling the QDs with different particle sizes and targets with functional groups (such as an amino) with specific surfaces. The method comprises: obtaining quantum dots with different fluorescent characteristics through separation and purification, namely, multi-color antibody markers, using the multi-color antibody markers as fluorescent probes, and establishing a reaction system for synchronous analysis of various antigen components of different kinds, thereby realizing the synchronous detection of multiple kinds of residues of the veterinary drug in animal food. Moreover, the method has the advantages of simple operation, high fluorescence intensity and long stabilization time.