Repeated epidemics caused by bacterial and fungal diseases pose a threat to global crop yields and food security, therefore, updating the structure of existing microbicides and improving the pesticide bioavailability are challenging tasks, perhaps planning to develop versatile supramolecular antimicrobial materials. Here, a low‐cost multifunctional supramolecular complex, named FT6@β‐CD, is constructed by host‐guest encapsulation of a thienyl‐engineered ingredient (FT6) into β‐cyclodextrin. This integrated architecture can significantly reduce the bounce and splash behaviors of droplets, improve the wetting performance, and eventually acquire excellent foliar deposition and targeted delivery. Whereafter, FT6@β‐CD can inhibit the transcription of type III secretion system (T3SS)‐associated genes, hypersensitive reaction, and final pathogenicity from a destructive pathogen Xanthomonas oryzae pv. oryzae (Xoo). Importantly, at a lower dosage of 200 µg mL−1, FT6@β‐CD presented excellent in vivo control effects (protection 48.1%, curative 50.1%) against Xoo, remarkably better than the commercial bactericidal formulation thiodiazole‐copper. Additionally, other supramolecular antifungal materials (FT24/FT25@HP‐β‐CD/β‐CD/Me‐β‐CD) constructed in this study can effectively treat Botryosphaeria dothidea and Botrytis cinerea with higher control efficiencies of 86.8% and 90.1% at 200 µg mL−1, respectively. This study provides a bright guidance for developing low‐cost, green, and eco‐friendly supramolecular microbicides for controlling agricultural diseases.