Based on high surface areas, adjustable porosity and microbicide activity, metal-organic frameworks (MOFs) HKUST-1 are widely used as drug release carriers for their slow degradation characteristics under slightly acidic conditions. In this work, porous HKUST-1 was reacted rapidly by cholinium salt (as the deprotonation agent and template) in an aqueous solution at room temperature. A novel antimicrobial system based on an imazalil encapsulated metal organic framework (imazalil IL-3@HKUST-1) was established. Imazalil IL-3@HKUST-1 could achieve synergism in inhibiting pathogenic fungi and bacteria. Moreover, six days after treatment, the slow and constant release of imazalil from imazalil IL@HKUST-1 exhibited better sustainability and microbicidal activity than imazalil. We believe that the method may provide a new strategy for related plant diseases caused by bacteria or fungi.