We investigated the structures and the stabilities of the three-membered rings FnX-CH2-Y (X = Si, P, S; Y = CH2, NH, O; n = 2 or 3) containing a hypervalent atom (X) and disclosed their origins by developing and applying an electron-pair bond model for hypervalent molecules. For the rings containing a pentacoordinated Si or P atom, the (ap, eq) isomers with the ring bonds in the apical and equatorial positions are local minima, while the (eq, eq) isomers with both ring bonds in the equatorial positions are the transition states of pseudorotation reactions due to the high ring strains. In contrast, the (ap, eq) and (eq, eq) isomers for the rings containing a tetracoordinated P or S atom are both local minima. The tetracoordinated species are less strained than the pentacoordinated ones because of the effect of the lone pair on X giving rise to less antibonding properties of the electron delocalization between the geminal ring bonds on X. Moreover, the more strained (eq, eq) isomers are surprisingly more stable than the (ap, eq) isomers in most of the tetracoordinated species. The relative stabilities are controlled by the repulsion between the lone pair on X and the apical bond. The relative stabilities of the (ap, eq) isomers with Y (= NH, O) in the apical and equatorial positions are predicted and discussed.