Polymer stimuli-responsive microgels find their use in various applications. The knowledge of its internal structure is of importance for further improvement and expanding the scope. Interpenetrating network (IPN) microgels may possess a remarkable feature of strongly non-uniform inner architecture, even microphase separation, in conditions of a selective solvent. In this research, we, for the first time, use a combination of static light scattering (SLS) and small-angle X-ray scattering (SAXS) techniques to collect the structure factors of aqueous dispersions of poly(N-isopropylacrylamide)-polyacrylic acid IPN microgels on the broad scale ofqvalues. We study the influence of solvent quality on microgel conformations and show that in a selective solvent, such a system undergoes microphase separation: the sub-network in a poor solvent conditions forms dense small aggregates inside the large swollen sub-network in a good solvent. We propose the microstructured sphere model for the IPN microgel structure factor interpretation and perform additional analysis and verification through coarse-grained molecular dynamics computer simulations.