The invention discloses a method for predicting the combined chronic toxicity of an antibiotic pollutant. The method comprises the following steps: 1, acquiring physical and chemical parameters of an antibiotic; 2, acquiring an acceptor protein, constructing a homologous model of the acceptor protein, and determining the mutual binding energy between the antibiotic and the acceptor protein; 3, determining the combined toxicity of the antibiotic; 4, establishing a prediction model for the chronic combined toxicity on the basis of the physical and chemical parameters of the antibiotic, the mutual binding energy between the antibiotic and the acceptor protein and the combined toxicity of the antibiotic; and 5, predicting the combined toxicity of the antibiotic through the model obtained in step 4. The method of the invention, which has the advantages of wide application range, no need of complex detection equipment, no test and environment pollution, and accurate prediction of the toxicity of the antibiotic composite pollutant, provides the scientific basis for the antibiotic pollutant discharge enforcement and the ecological risk evaluation.