Precise mapping of structural heterogeneity at the sub-10 nm scale is pivotal for rational nanoparticle design, yet conventional analytical workflows remain inadequate. Here we integrate dilution-controlled asymmetric flow field-flow fractionation (AF4) with small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) to interrogate ellipsoidal solid-liquid lipid nanoparticles (LNPs). The dilution-controlled AF4 mode amplifies scattering contrast, enabling robust, shape-resolved analysis across entire elution profiles. Coupling AF4 to SANS in DO further sharpens resolution for the smallest fractions by reducing particle diffusion through increased solvent viscosity. Comparative sizing shows that SAXS/SANS accurately capture primary particles down to ∼5 nm, whereas multi-angle light scattering chiefly detects loosely associated aggregates. Morphology profiling reveals that surfactant identity governs particle shape, polydispersity, and overall architecture. Joint SAXS/SANS modeling uncovers a 2-3 nm polar shell enveloping an internal core-shell morphology. Together, these insights refine our understanding of LNP size, morphology and drug localization and establish dilution-controlled AF4-SAXS/SANS as a high-resolution platform for dissecting complex nanoparticle systems relevant to biomedical applications. 2