S-omeprazole　and　R-rabeprazole　are　important　proton　pump　inhibitors　(PPIs)　used　for　treating　peptic　disorders.　They　can　be　biosynthesized　from　the　corresponding　sulfide　catalyzed　by　Baeyer-Villiger　monooxygenases　(BVMOs).　During　the　development　of　BVMOs　for　target　sulfoxide　preparation,　stereoselectivity　and　over-　oxidation　degree　are　important　factors　considered　most.　In　the　present　study,　LnPAMO-Mu15　designed　previously　and　TtPAMO　from　Thermothelomyces　thermophilus　showed　high　(S)-　and　(R)-configuration　stereoselectivity　respectively　towards　thioethers.　TtPAMO　was　found　to　be　capable　of　oxidating　omeprazole　sulfide　(OPS)　and　rabeprazole　sulfide　(RPS)　into　R-omeprazole　and　R-rabeprazole　respectively.　However,　the　overoxidation　issue　existed　and　limited　the　application　of　TtPAMO　in　the　biosynthesis　of　sulfoxides.　The　structural　mechanisms　for　adverse　stereoselectivity　between　LnPAMO-Mu15　and　TtPAMO　towards　OPS　and　the　overoxidation　of　OPS　by　TtPAMO　were　revealed,　based　on　which,　TtPAMO　was　rationally　designed　focused　on　the　flexibility　of　loops　near　catalytic　sites.　The　variant　TtPAMO-S482Y　was　screened　out　with　lowest　overoxidation　degree　towards　OPS　and　RPS　due　to　the　decreased　flexibility　of　catalytic　center　than　TtPAMO.　The　success　in　this　study　not　only　proved　the　rationality　of　the　overoxidation　mechanism　proposed　in　this　study　but　also　provided　hints　for　the　development　of　BVMOs　towards　thioether　substrate　for　corresponding　sulfoxide　preparation.