The soft–hard-donor-combined phosphonate-based ligands are one of the popular extractants for the separation of actinide from lanthanide in nuclear waste management. Among them, tetradentate phenanthroline-derived phosphonate (POPhen) ligands attract much attention. A recent report suggests that n-butyl substituted POPhen shows better portioning behaviour compared to its ethyl derivative. However, the effect of the alkyl chain on the extraction and complexation behaviour is yet to be explored. We addressed this issue by designing POPhen ligands with alkyl chains of different lengths (methyl to n-hexyl) using DFT calculations. Results show that the n-butyl substituted ligand has an excellent extraction capability with high selectivity towards Am(III) over Eu(III) ion. Electronic structure studies demonstrate that MN and MO bond lengths are greater in the Eu complexes than the corresponding Am complexes. Atoms in Molecules analysis was done on the optimized geometries to ascertain the nature of interactions present in these ML(NO3)3 complexes. In addition, bond order analysis reiterates that the n-butyl substituted ligand is having a better extraction ability towards Am(III) ions through higher MO and MN bond orders. The calculated separation factor of the ligand with n-butyl substitution is greater than that of other ligands. Increasing the length of the alkyl chain until the n-butyl increases the selectivity and binding, beyond which, the chain length is not of much use in improving the selectivity as well as the binding ability of these POPhen ligands. This work brings out an ideal alkyl chain length (n-butyl) required for better binding and extraction capability of POPhen ligands. Overall this computational study sheds light on the need for tailoring ligands with optimum alkyl chain for effective lanthanide/actinide separation.