We have theoretically investigated the mechanism and origin of stereoselectivity in N-heterocyclic carbene (NHC)-catalyzed NH functionalization/cycloaddition reaction of indole aldehyde and ketone. The outcome of theoretical study shows that the formal [4 + 2] cycloaddition determines the stereoselectivity and the formation of R-configured product is more favorable, which aligns with the experimental results. The stronger interaction between two interactive fragments disclosed by distortion/interaction analysis governs the stereoselectivity. The types and strength of such interaction are further qualitatively and quantitatively recognized by NCI and AIM analyses.