In this study, hydroxycalix[4]arene, hydroxycalix[5]arene, hydroxycalix[6]arene, and their complexes with uranyl and thorium ions were analyzed by density functional theory. The coordination ability of hydroxycalixarene ligands to uranyl and thorium ions could be analyzed by simulating the infrared and ultraviolet–visible spectra, the Wiberg bond energy levels, the energy gaps, and the binding energies. We found that various hydroxycalixarene complexes with uranyl or thorium ions had significant differences in their properties, as well as in their infrared vibrational and ultraviolet absorption spectra. More importantly, different hydroxycalixarenes can be selected based on the adsorption requirements in environments with coexisting uranium and thorium ions. For example, hydroxycalix[4]arene and hydroxycalix[5]arene had a significantly higher binding capacities for thorium than uranyl ions, while hydroxycalix[6]arene showed less of a difference for the two ions but had a good binding ability for both uranyl and thorium ions at the same time. Thus, the use of hydroxycalixarene can achieve the removal of both uranyl and thorium ions in the environment, and the use of specific hydroxycalixarenes may be able to achieve the separation of these ions. These results provide important guidance for the future research of hydroxycalixarene without requiring the synthesis of hydrophilic derivatives, and they may be directly applied to the field of heavy metals.