Functional magnetic nanoparticles have attracted increasing interest for applications in environmental remediation, drug delivery, and biomedicine due to their tunable interfacial properties and magnetic responsiveness. The layer-by-layer (LBL) assembly of polyelectrolyte shells provides an effective strategy to enhance colloidal stability, dispersibility, and interparticle interactions. The performance of LBL-modified magnetic nanoparticles is influenced by the number of polyelectrolyte layers, yet their precise and systematic structural characterization remains insufficient. Moreover, their structural evolution under dynamic shear conditions is still poorly understood due to the limited availability of in situ analytical methods. Here, we present an integrated platform that couples small-angle neutron scattering (SANS), a rheometer, and dynamic light scattering (DLS) to investigate the microstructural changes of Fe₃O₄ nanoparticles coated with varying LBL shell thicknesses (N0–N3) under continuous shear. Although the rheological properties of the dispersions remain relatively unchanged during shear, the use of a rheometer effectively suppresses nanoparticle sedimentation, enabling stable and accurate SANS measurements. We systematically analyzed both the time-resolved SANS profiles collected every 20 minutes and the cumulative data obtained over the full duration of the shear process, in correlation with time-dependent viscosity and hydrodynamic size data from rheometry and DLS. The results reveal that uncoated N0 particles tend to undergo irreversible aggregation, while single-layer coated N1 particles remain well-dispersed with minimal structural change. In contrast, thicker coatings (N2 and N3) exhibit more pronounced aggregation and sedimentation in the absence of shear. However, under shear, large aggregates are rapidly disrupted and eventually stabilize into smaller aggregate sizes. SANS data were analyzed using a combination of sphere or core–shell sphere models with hard-sphere or sticky hard-sphere structure factors, along with unified power-law fitting. By comparing different model combinations, we assessed their influence on fitting results. The data show a consistent core radius (~71.15 ± 0.15 Å) across all samples and a linear increase in shell thickness per added layer (~20.75 ± 0.42 Å). The Stickiness parameter was uniformly set to 0.5, and the perturbation remained ≤0.1, indicating that all fitted parameters are physically meaningful and consistent with the expected structural features of the system. This study demonstrates the potential of coupling SANS with rheology and DLS for high-resolution, in situ monitoring of nanoparticle structural changes. In particular, the use of a rheometer during SANS measurements effectively eliminates concentration gradients caused by particle sedimentation, thereby improving measurement accuracy. This integrated platform significantly expands the applicability of SANS to structurally complex and dynamically evolving colloidal dispersions. Furthermore, this coupled characterization platform offers promising opportunities for elucidating the underlying mechanisms and kinetics during the synthesis of nanomaterials.