 Partial manganese substitution of iron in ferrous carbonate (MnxFe1−xCO3, x = 0, 0.1, 0.2, 0.3) is obtained via a one-step hydrothermal method. The phase structure, morphology, and structural stability are characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), and thermogravimetric analysis, respectively. The results of XRD demonstrate that Mn-doping does not obviously change the phase structure. MnxFe1−xCO3 possesses cockscomb-like and tunnel structures observed by SEM images. Meanwhile, the results of XPS further demonstrate the existence of Fe2+ and Mn2+. Mn-doped FeCO3 samples remarkably improve galvanostatic charge–discharge stability and rate capability as anode materials for lithium-ion batteries because of the synergistic behavior of Fe2+ and Mn2+ with cockscomb-like and tunnel structures. MnxFe1−xCO3 (x = 0.2) as an anode material delivers an initial specific discharge capacity of 2400 mAh g−1 at 200 mA g−1 and 904 mAh g−1 over 100 cycles. Therefore, MnxFe1−xCO3 anode materials are promising for lithium-ion batteries because of their low-cost preparation, environmentally friendly nature, and excellent electrochemical performance.