Patulin is a neurotoxin with a strong toxic effect. This toxin is expensive and unstable; the chemical structure of patulin is simple, and the direct preparation of immunogens from patulin has a poor immune effect. As a result, few immunoassay methods for patulin have been reported. Design and preparation of the immunogen is one of the key steps for developing the immunoassay. Here, the structural characteristics of patulin were studied via computer-aided simulation design and methods for virtual screening of drug molecules. A suitable substitute with low toxicity and cost was optimized and screened, and the hapten of patulin was designed and successfully prepared. Two immunogens of patulin were obtained by conjugation with two carrier proteins (BSA and KLH) by the active ester method. The polyclonal antibodies were prepared after the immunization of rabbits, and the antiserum titers reached 1:16000 and 1:64000, respectively. This study lays a foundation for the further establishment of an immunoassay for patulin and also provides new ideas and methods for designing immunogens for toxic small-molecule compounds.