The heating effect in the temperature interval of 20―70 °C on the aggregate structure in aqueous ferrofluids is analyzed basing on the data of small-angle X-ray (SAXS) and neutron (SANS) scattering. Samples prepared according to the same stabilization procedure (double-layer surfactant coating) but with different dispersed magnetic materials (magnetite and cobalt ferrite) show different temperature sensitivity. A temperature-induced reorganization from developed aggregates to elongated chain-like aggregates is revealed by observing changes in the scattering curves, which are considered in the frame of the fractal concept. In addition to the determination of fractal dimension, the accent is also given to the cut-off effect in the scattering curves induced by the finite aggregate size. The scattering model is chosen from the available approaches basing on the analysis of the dimension-dependent universal parameter of the average aggregate form-factor, which continuously changes with varying temperature. The particle polydispersity is taken into account. The contrast variation based on isotope (H/D) substitution in solvent is done in SANS experiments to conclude about the structural organization of magnetic particles and surfactant component in the systems.