The removal of pesticide residues from fruits reduces the risk of pesticide exposure in humans. In this study, carbosulfan and trichlorfon residues removed from apple using ozone-microbubble treatment (OMBT), tap water, hypochlorous acid-water, ozone-water, and microbubble-water. The pesticide removal rates by OMBT ranged between 98% and 100%. In addition, OMBT had little effects on apple surface color. In addition, this work evaluated the interaction between apple matrix and pesticide molecules, including the binding sites and adsorption energy, and proposed a possible adsorption mechanism. OMBT is an effective technique for removing pesticide residues from fruits. The removal effect of pesticides may be related to the matrix components on the surface of fruits.