The invention discloses a method for detecting bacterial drug resistance in aquaculture, which comprises the following steps: (1) an antibacterial drug stock solution is prepared; (2) a bacterial liquid is prepared; (3) an antibiotic working solution is prepared from the antibacterial drug stock solution obtained in step (1); (4) a 96-well microtitration plate is placed in an incubator for incubation; and (5) data are read through a microplate reader for analysis. The method applies to bacterial drug resistance detections in aquaculture and other areas. In combination of the specification of the 96-well microtitration plate (8 multiply 12) and the drug concentration scope required by CLSI (Clinical and Laboratory Standards Institute), 8 categories of antibiotic drugs and 10 concentration gradients are selected for detection. When the method is in use, no flat plate is required, the steps of configuring a large amount of culture mediums, manufacturing drug sensitive paper scraps and measuring the inhibition zone are spared, and a small quantity of culture solutions is required. The method has the advantages of strong practicability, convenience, accuracy and stability in results, good repeatability and high sensitivity.