α-heterosubstituted 1,3-dioxane and 1,3-dithiane systems have been extensively reported for n_( X) → σ_(C-Y)^* (X, Y = heteroatoms) hyperconjugative interactions. However, the definitive interpretation for the conformational analysis of 2-carbomethoxy 1,3-diheterocyclohexane is less explored. The weaker accepting ability of C-C(carbomethoxy) antibonding orbitals in 2-substituted 1,3-diheterocyclohexane makes it an attractive candidate for estimating the role of stereoelectronic effects in such systems. This study explores conformational preferences of 2-carbomethoxy substituted 1,3-dioxane, 1,3-oxathiane and 1,3-dithiane in the light of stereoelectronic interactions and the contribution of other factors to attain stability in the respective systems. The DFT calculated results in the solvent phase reveal the delocalizing interactions operate in all the three systems examined; however, ring strain override the axial preference of 2-carbomethoxy substituent on 1,3-dioxane (2-ax) and 1,3-oxathiane (3-ax). The hyperconjugative interaction, lower ring strain and attractive C-H∙∙∙O non-bonded interactions favor axial (4-ax) over equatorial (4-eq) isomer of methyl-2-carboxylate-1,3-dithiane.