We are reporting a novel synthetic approach to prepare organic modified Ba-hexaferrite nanocrystals with controlled size and morphology under a supercritical water (SCW) flow reactor process. The surface of the Ba-hexaferrite nanocrystal was capped with oleic acid ligand to control the particle growth, size, and morphology. The results showed that the concentration of oleic acid reagent played a key role in controlling the cubic and octahedral shape of Ba-hexaferrite nanocrystals. This indicates that the size and morphology of nanocrystals were greatly influenced by the organic modification under the SCW process, resulting in a drastic reduction in the particle size from 30 to 9 nm. The organic ligand capped Ba-hexaferrite nanocrystals exhibit a higher coercivity (about 2800 Oe) at 5 and 280 K temperature. This study provides a novel approach for large-scale production of complex metal oxide colloidal nanocrystals with uniform size, well-defined shape, and controlled surface chemistry.