The distinctive cavity structure of cyclodextrin, which results in binding properties, is credited with its application prospects in chemical, pharmacy, and material fields. The binding capacity can be regulated by substituting the hydroxyl groups on the cyclodextrins. It is possible to acquire anticipated binding properties by designing the modified groups on cyclodextrins. In this article, a data-driven model is proposed with a novel cyclodextrin/guest structure representation method to assist the cyclodextrin design. The model's performance is verified via several validations, as the squared correlation coefficients for cross-validation (Q2) and test set (R2test) are 0.801 and 0.841, respectively. With the proposed model and fluorescence experiments for cyclodextrin/bisphenol complexes, several cyclodextrin hosts, which have a strong binding capacity for bisphenols, are screened, synthesized, and characterized. The results show a controlled average absolute error of 0.605 M-1, suggesting the feasibility of data supplementation and molecular design. It is believed that the data-driven model can serve as theoretical assistance and a driving tool for the cyclodextrin complexes design, potentially leading to advancements in cyclodextrin's industrial applications and scientific research.