Carvacrol has strong antibacterial and antiinflammatory effects and has been increasingly employed in the food and pharmaceutical industries. However, carvacrol is volatile, easily oxidized, and difficult to dissolve in water. In this study, carvacrol was encapsulated with mixed cyclodextrins during enzymatic cyclodextrin synthesis and microencapsulated carvacrol was obtained by spray drying. The encapsulation efficiency and encapsulation yield of microencapsulated carvacrol were 92.16% and 72.30%, respectively. The encapsulation yield for the pure β-cyclodextrin/carvacrol inclusion complex (38.96%) was lower than that of microencapsulated carvacrol (50.44%) when the guest/host ratio was 1:4. No significant difference ( P > 0.05) in the amount of encapsulated carvacrol was found when the guest/host ratio was less than 1:6. Microencapsulated carvacrol appeared in scanning electron micrographs as spherical particles with obvious invaginations. Determination of the inclusion formation constant, NMR analysis, and molecular modeling revealed that cavity size affected the ability of cyclodextrins to include carvacrol. Finally, the rate constants ( k ) of carvacrol release from microencapsulated carvacrol (1.09–8.53 × 10 −4 ) at various temperatures and relative humidities were systematically lower than those of β-cyclodextrin/carvacrol inclusion complexes (5.20–199 × 10 −4 ). This study transcended traditional essential oil-cyclodextrin inclusion formation by developing a mixed-cyclodextrin inclusion compound that achieved better encapsulation and superior release. • Carvacrol increased the yield of enzymatically produced cyclodextrins. • Mixed cyclodextrins encapsulated carvacrol with high encapsulation yield and superior release. • Their cavity sizes affected the ability of cyclodextrins to include carvacrol.