Microscopic structures in liquid-liquid extraction, such as structuration between extractants or extracted complexes in bulk organic phases and at interfaces, can influence macroscopic phenomena, such as the distribution behavior of solutes, including extraction efficiency and selectivity. In this study, we correlated the macroscopic behavior of the Zr(IV) extraction from nitric acid solutions with microscopic structural information to understand at the molecular level the key factors contributing to the higher metal ion extraction performance in the fluorous extraction system as compared to the analogous organic extraction system. The fluorous and organic extraction systems consist of tris(4,4,5,5,6,6,7,7,7-nonafluoroheptyl) phosphate (TFP) in perfluorohexane and tri-n-heptyl phosphate (THP) in n-hexane, respectively. Extended X-ray absorption fine structure, neutron reflectometry (NR), and small-angle neutron scattering revealed the structural information around the central metal ion of the complex, at the interface, and in the bulk extraction phase, respectively. NR results showed that extractant molecules did not accumulate much at the interface in both extraction system. In the fluorous extraction system, extractant aggregates with a 1.46 nm radius of gyration (Rg) were formed after contact with nitric acid, and remained even after Zr(IV) extraction through the form of a 1:3 (Zr(IV):TFP) complex. In contrast, in the organic extraction system, only extractant dimers with Rg of 0.70 nm were formed and Zr(IV) is extracted through the form of a 1:2 (Zr(IV):THP) complex. We speculate that differences in the local coordination structure around the Zr(IV) ion and the structuration of the extractant molecules in the bulk extraction phase contribute to the high Zr(IV) extraction performance in the fluorous extraction system. In particular, the size of the aggregates hardly changed with increasing Zr(IV) concentration in the fluorous phase, which may be closely related to the absence of phase splitting in the fluorous extraction system.