The kaolin was modified by ball-milling method, using poly (methyl hydrosiloxane) (PMHS) as a hydrophobic modifier. Subsequently, immobilization of emamectin benzoate onto the modified kaolin particles was carried out by freeze-drying technology, and then the drug-loaded clays were encapsulated in Alginate matrix to form modified kaolin-calcium alginate composite microgel beads (MKL-CA-CMBs). The structure, morphology and property of the modified kaolin were characterized by laser particle size and zeta potential analyzer, FTIR, SEM, XRD, Specific surface area and pore size analyzer. Simultaneously, the drug-loaded property and release performance of MKL-CA-CMBs were also investigated. Experimental results showed that PMHS was absorbed onto the surface of kaolin via physical adsorption or chemical adsorption under the mechanical action of ball-mill. After the modification of kaolin, its size decreased, specific surface area and hydrophobicity increased, beneficial to the load of hydrophobic organic pesticide, making the drug loading rate (DLR) and encapsulation efficiency (EE) of kaolin-calcium alginate composite microgel beads (KL-CA-CMBs) upgrade from 6.5% and 53.1% to 9.7% and 72.5%, respectively. The slow-release performance of MKL-CA-CMBs was mainly based on the affinity of MKL to hydrophobic organic pesticide, and the release model of the formulation belonged to the Non-fickian diffusion model.