Baeyer-Villiger monooxygenases (BVMOs) can catalyze the asymmetric oxidation of sulfides to valuable chiral sulfoxides, but the overoxidation of sulfoxides to undesired sulfones limits the synthetic application of BVMOs. This overoxidation is caused by insufficient substrate selectivity of BVMOs, where the desired product sulfoxide can be further oxidized. In this study, a mathematical model was constructed to quantitatively define the substrate selectivity based on the ratio of the specificity constant (kcat/Km) between sulfide and sulfoxide. The substrate selectivity of a pyrmetazole monooxygenase (AcPSMO) was precisely regulated using a structure-guided substrate tunnel engineering approach, which successfully minimized sulfoxide overoxidation. The sulfone content of variant F277L was less than 1% (mol/mol), compared with 65% for the wild-type, in the pyrmetazole oxidation reaction after 24 h. Molecular dynamics simulations and quantum mechanics/molecular mechanics studies showed that the altered H-bonding networks surrounding the flavin hydroperoxide (FADH-OOH) can modulate the mechanism and activity for sulfoxide oxidation. Furthermore, the redesigned mutants of AcPSMO were successfully applied for the controllable synthesis of other chiral prazole sulfoxides.