Asymmetric olefin isomerization of β,γ- to α,β-unsaturated butenolides catalyzed by novel cinchona alkaloid derivatives was investigated in-depth using density functional theory (M05-2x and B2PLYP-D). Three possible mechanistic scenarios, differing in the binding modes of the substrate to the catalyst, have been evaluated. Computations revealed that both the protonated quinuclidine and the 6'-OH of catalysts may act as the proton donor in the stereocontrolling step. Variation of the catalytic activity and enantioselectivity by tuning the electronic effect of catalyst was well reproduced computationally. It suggested that, for certain acid-base bifunctional chiral catalysts, the acid-base active sites of catalysts may interconvert and give new catalyst varieties of higher activity and selectivity. In addition, the noncovalent interactions in the stereocontrolling transition-state structures were identified, and their strength was quantitatively estimated. The weak nonconventional C-H···O hydrogen-bonding interactions were found to be crucial to inducing the enantioselectivity of the cinchona alkaloid derivatives catalyzed asymmetric olefin isomerization. The computational results provided further theoretical evidence that the rate-limiting step of this bioinspired organocatalytic olefin isomerization is inconsistent with that of the enzyme catalyzed olefin isomerization.