The effect of the amorphous structure and nanocrystalline nature of metal oxide on its anode performance in lithium ion batteries is investigated with two nanocrystalline and one well-crystallized layered manganese oxides. X-ray amorphous manganese oxide nanocrystals are synthesized by soft-chemical redox reactions using reducing agents of KBH4 and LiI at room temperature, whereas well-crystallized layered manganese oxide is obtained by solid state reaction at elevated temperature. Although both of the amorphous manganese oxides lack a long-range structural order, they are crystallized with a layered MnO2-type local structure, which is nearly identical to the crystal structure of the well-crystallized K0.45MnO2. In comparison with the well-crystallized K0.45MnO2, both the amorphous manganese oxides commonly possess smaller particle sizes with larger surface areas and better homogeneity of composite structure. The amorphous manganese oxide nanocrystals show better anode performance with greater discharge capacity for lithium ion batteries than does the well-crystallized K0.45MnO2, which is attributable to the greater surface area, higher structural and electrochemical stability, more homogeneous composite structure, and better charge-transfer characteristics of the amorphous materials. This result highlights the merit of the nanocrystalline and amorphous nature for optimizing the electrode performance of manganese oxide. The present solution-based redox reaction can provide a facile, economic, and scalable route for synthesizing efficient manganese-based anode materials for lithium ion batteries.