The mechanism and origin of stereoselectivities in N-heterocyclic carbine (NHC)-catalyzed [3 + 2] cycloaddition of 3-bromoenals and isatin N-Boc ketimines have been studied using density functional theory (DFT) calculations. Various possible reaction pathways were examined and analyzed. Our calculation results reveal that the catalytic cycle can be characterized by six steps: nucleophilic attack of a catalyst on 3-bromoenal (step I); [1,2]-proton transfer (step II); addition to the other reactant isatin N-Boc ketimine (step III); debromination (step IV); intramolecular cycloaddition concerted with hydrogen-elimination (step V) and elimination of the NHC catalyst (step VI). For step II, besides the direct [1,2]-proton transfer, the mediator (base and water)-assisted proton transfer has been investigated, and the DFT results show that the 2H2O cluster-mediated proton transfer is most energy favorable. The carbon-carbon bond formation step (step III) is calculated to be the stereoselectivity-determining step and the S-configuration product is the predominant product, which are in good agreement with the experimental observations. The mechanistic insights gained in this work should be helpful for other NHC-catalyzed reactions.