The development of novel, safe, and efficient pest and disease control technologies for agricultural crops remains a pivotal area of research. In this study, by combining ZIF-8 and ZIF-90, a water-stable, pH-responsive bilayer MOF nanoparticle (NP) named Z8@Z90 was created, and tebuconazole (TEB) was added to form T@Z8@Z90, used for controlling peanut southern blight. The loading efficiency of TEB within the T@Z8@Z90 reached 26.15%, enabling rapid release in acidic environments triggered by oxalic acid (OA) secreted by Sclerotium rolfsii. In vitro experiments showed that T@Z8@Z90 can regulate the oxalic acid secretion of S. rolfsii and destroy its cell membrane structure. Additional experiments revealed that T@Z8@Z90 reduced sclerotial formation, decreased the total protein content of sclerotia, and influenced their sensitivity to pesticides, thereby mitigating the risk of reinfection by S. rolfsii. Notably, T@Z8@Z90 exhibited efficient translocation within peanut seedlings, being absorbed through the roots and transported to the leaves. At a concentration of 200 mg/L, T@Z8@Z90 exhibited high safety profiles for peanut seedling growth compared to the TEB suspension. Moreover, T@Z8@Z90 is safer for earthworms than TEB SC. Overall, this study offers valuable insights for the management of soil-borne diseases in agriculture and contributes to the advancement of sustainable agricultural practices.