Cholesterol oxidase catalyzes the oxidation and isomerization of the cholestane substrates leading to the addition of a hydroxyl group at the C3 position. Rational engineering of the cholesterol oxidase from Pimelobacter simplex (PsChO) was performed. Mutagenesis of V64 and F70 improved the catalytic activities toward cholestane substrates. Molecular dynamics simulations, together with structure-activity relationship analysis, revealed that both V64C and F70V increased the binding free energy between PsChO mutants and cholesterol. F70V and V64C mutations might cause the movement of loops L56-P77, K45-P49 and L350-E354 at active site. They enlarged the substrate-binding cavity and relieved the steric interference with substrates facilitating recognition of C17 hydrophobic substrates with long side chain substrates.