In this work, Co-doped SnO2 powders were synthesized via a simple hydrothermal process without using any surfactants. A detailed microstructural analysis showed that incorporation of Co (H) ions distorts the SnO2 lattice. The unit cell volume becomes smaller as the nominal Co content increases. Neither segregated secondary phases nor the Co-rich clusters were detected. The particles of Co-doped SnO2 self-assembled from low-dimensional building blocks and acquired a three-dimensional hierarchical structure. The dependencies of the magnetic characteristics of the synthesized Co-doped SnO2 on the concentration of Co are nonlinear. The highest saturation magnetization (3.5 emu/g) of the flower-like structures was found in the material with a Co/SnO2 mass ratio of 0.06. One of the reasons for the enhancement of room-temperature ferromagnetism in the Co-doped SnO2 is an anisotropic growth of SnO2 crystals in the presence of Co (II) ions, which serve as a structure-controlling agent for the growing crystals.