Nanopowders of the magnetite-maggemite series were synthesized by both aqueous precipitation and using sol-gel technology. A comprehensive comparative study of the structure of the synthesized powders was carried out using the methods of X-ray phase analysis (XPA), scanning electron microscopy (SEM), low-temperature nitrogen adsorption and small-angle polarized neutron scattering (SAPNS). It has been established that the synthesized iron oxide nanopowders are porous systems that, depending on the synthesis method, have a one-level or two-level (for powders obtained by aqueous synthesis) and three-level (for powders obtained by the sol-gel method) hierarchical structure organization with different characteristic scales and types of aggregation for each from structural levels, and the characteristic size for the larger level in both cases exceeds 45 nm. It was revealed that the magnetic structure of the obtained iron oxide powders, regardless of the synthesis method, consists of superparamagnetic particles with a characteristic magnetic radius R_М ≈ 4 nm and magnetic-nuclear cross-correlations R_MN ≈ 3 nm for powders obtained by the sol-gel method; and with R_M ≈ 5–11 nm and R_MN ≈ 4–8 nm for powders obtained by aqueous synthesis, depending on the production conditions.