This research aimed at exploring the stabilities of conformers of 1,4-dioxane-2,3-bis(pyridin-1-ium) and 1,4-dioxane-2,5-bis(pyridin-1-ium) molecules at the B3LYP/6-311+G(d,p) theory level. To this goal, estimations of the total energies and dipole moments of the axial and equatorial conformations were first done for the mentioned molecules. C-N and C-O bond distances were calculated and these variations were explained with the negative hyperconjugative anomeric effects. The negative hyperconjugative anomeric effect on the axial conformer was illustrated by NBO analysis and the interactions responsible for the effect were explored. Also, QTAIM study was used for illustration of the C-N and C-C bonds in the studied systems.