We consider a structural and thermodynamic analysis of uranium solvent extraction by tertiary amines for which the alkyl chain configuration has been modified. The first part of this work revealed that tertiary amines with longer or branched alkyl chains allow tuning the phase stability and uranium extraction by modifying the volume of the polar species extracted in the organic phase. A complete fit of SANS data confirms in this second part that this phenomenon is related to the supramolecular self-assembly of the tertiary amines into smaller reverse micelle like aggregates for longer or branched alkyl chains. It moreover shows that these smaller aggregates quench third phase formation thanks to reduced attractive interactions between them. A thermodynamic analysis based on the “ienaic” approach further rationalizes this effect by showing that alkyl chains have a significant effect on the aggregate’s curvature free energy. The latter becomes a predominant inhibitor of uranium free energy of transfer due to the high entropic contribution originated by the extractants branching and packing.