The comparative study of three calix[4]heterocycles (calix[4]pyrrole, calix[4]furan, and calix[4]thiophene) has been theoretically performed by using high-level density functional theory (DFT) at the MPWB1K/6-311G$^{**}$//B3LYP/6- 311G$^{**}$ level. The effect of different hetero-atoms (nitrogen, oxygen, and sulfur) placed in the heterocycles on the conformational flexibility, thermodynamic stability order, cavity sizes, charge distributions, and binding propensities are examined. The thermodynamic stability differences between the conformers are found to be much greater in calix[4]pyrrole compared to those in calix[4]furan and calix[4]thiophene. Relatively larger NH group and higher dipole of a pyrrole ring in calix[4]pyrrole contribute to the higher energy barrier for the conformational conversions and relatively rigid potential energy surface compared to the case of calix[4]furan and calix[4]thiophene. The computational results herein provide theoretical understanding of the conformational flexibility and the thermodynamic nature which can be applied to understand the complexation behavior of the three calix[4]heterocycles.