Skim milk concentrates have important applications in the dairy industry, often as intermediate ingredients. Concentration of skim milk by reverse osmosis membrane filtration induces water removal, which reduces the free volume between the colloidal components, in particular the casein micelles. Thermal treatment before or after concentration impacts the morphology of casein micelles. These changes affect the flow behavior and viscosity, but the consequences for supermicellar structure have not been elucidated. In the present study, skim milk concentrates with different total solid contents from 8.7% (control) up to 22.8% (w/w), prepared by reverse osmosis membrane filtration of non-heated and pasteurized skim milk, were heat treated at 75 °C for 18 s, and compared with non-heated concentrates. The structure of the concentrates was studied using Ultra Small Angle X-ray Scattering (USAXS), and the viscosity of concentrates was measured. The USAXS intensity I(q) was fitted at small and intermediate q-regions (0.0005 < q < 0.003 Å⁻¹ and 0.0035 < q < 0.03 Å⁻¹, respectively) with a power law. The value of the power law exponent was used to assess the heat- and concentration-induced aggregation of the milk solids and correlate it with the apparent viscosity. The results showed that increased viscosity of skim milk concentrates, due to water removal and heat-load, can be explained by increased aggregation of the casein micelles into elongated aggregates and increased smoothening of the casein micelle surface.