Ternary metal oxides have been considered a promising anode material for lithium-ion batteries (LIBs) based on their stable chemical compositions and abundant active sites. This work doped Mn into BaFe12O19 by a simple hydrothermal method and subsequent annealing treatment. By adjusting the ratio of raw materials, we obtained a Mn-doped BaFe12O19 electrode with an irregular hexagonal morphology. The doped Mn ions are in + 2, + 3, and + 4 valence states. Due to the octahedral position preference, Mn2+ tends to occupy the tetrahedral position. At the same time, Mn4+ favors octahedral coordination, and most Mn resides in (distorted) octahedral coordination in the form of + 3 valence state. Employed as a LIB anode, the specific capacity of the electrode reached 782.57 mA h g−1 after 150 cycles at a current density of 100 mA g−1. Even at a high current of 1 A g−1, the specific capacity remained at 439.99 mA h g−1 after 450 cycles. Mn-doped BaFe12O19 exhibited better cycling stability and electrochemical performance compared with pure BaFe12O19, which may be attributed to significantly enhanced charge transport kinetics at the interface between electrodes and electrolytes by Mn doping.