Extraction mechanisms of two bifunctional extractants which differ only by the grafting of an alkyl chain between their two functions were investigated at molecular and supramolecular scales to investigate the origin of their very different separation factors toward uranium and zirconium. Investigation of the complex structure with spectroscopic analysis (Fourier Transform Infra-Red (FTIR), ElectroSpray Ionization Mass Spectroscopy (ESI-MS) and Extended X-Ray Absorption Fine Structure (EXAFS)) demonstrated that alkylation does not affect the chelation mechanism of uranium and zirconium. Stoichiometries of complexes remain identical for both extractants: UO2L2(NO3)2 and zirconium polynuclear complexes are formed after extraction into the organic phase. The origin of selectivity was therefore investigated by considering the supramolecular self-assembly of the two bifunctional molecules. Small-Angle X ray and Neutrons Scattering (SAXS and SANS) showed that the highest separation factors between U and Zr are obtained when smaller aggregates are formed. The results of this study therefore suggests that the selectivity is controlled by the supramolecular self-assembly of the two extractant molecules. Thanks to a smaller packing parameter, the non-alkylated molecule forms bigger aggregates analogous to reverse micelles that can extract additional polar species in their polar core through a solubilization effect, thus decreasing the separation factor between uranium and zirconium.