In this work, we report an energy decomposition and electronic structure analysis using DFT calculations for the C-C coupling step in the Henry reaction with cinchona thiourea as catalyst and DMF solvent to unravel the origin of enantioselectivity. We found that the conformation of flexible thiourea moiety is affected by the solvent, and in the preferred conformation of thiourea in strong Lewis basic DMF solvent, the N-H sites are in the opposite direction, i.e., in trans conformation. Hence, the thiourea moiety acts via single hydrogen bonding with substrates. The conformation of the substrates with respect to the forming C-C bond plays critical role to increase orbital interaction between two substrates and enhances hydrogen bond strength between substrates and catalyst, which in turn stabilizes the positive charge developing on the catalyst at the transition state for one of the enantiomers (S). Thus, the enantioselectivity has electronic structure origin. The stronger H-bond formation in the S enantiomer has been confirmed by the calculated IR spectra and is in agreement with thus far experimental and computational results.