Manganese oxalate is a low-cost and high-capacity anode for lithium-ion batteries (LIBs). However, its performance is limited by the low conductivity and the volume change during charge/discharge processes. Herein, polymorphic manganese oxalates were controllably synthesized by a solvothermal process. Monoclinic α-MnC2O4·2H2O with space group C2/c can be prepared with the reactant concentration below 0.2 mol·L−1, while orthonormal MnC2O4·3H2O with space group Pcaa can be prepared with the reactant concentration above 0.2 mol·L−1. After removing crystal water, MnC2O4·2H2O and MnC2O4·3H2O are transformed into orthonormal MnC2O4. When the reactant concentration increases from 0.1 to 0.3 mol·L−1, manganese oxalate changes from rods to cubes, and its specific surface area and pore volume first increase and then decrease. Mesoporous MnC2O4 rod prepared at 0.2 mol·L−1 has a larger specific surface area and pore volume. This rod-like sample can maintain 920 and 790 mAh·g−1 after 300 cycles 2 and 5 A·g−1, respectively, exhibiting higher specific capacity, better cycle stability, and better rate performance. Therefore, the prepared mesoporous MnC2O4 rod can potentially apply in high-energy–density LIBs.