Two types of hierarchical mesoporous urchin-like Mn3O4/carbon microspheres (HM-MO/C-MS) have been prepared via the in situ carbonization of the newly synthesized lamellar manganese alkoxide (Mn-DEG) along with the crystallization of Mn3O4 in air (MO-A) and nitrogen (MO-N), respectively. Such unique HM-MO/C-MS with high surface area provides obvious advantages including a large contact area with electrolyte, a short transport path for Li+ ions, a low resistance for charge transfer, and a superior structural stability. When used as an anode material for lithium ion batteries in the voltage range of 0.01–3V, the HM-MO/C-MS obtained in nitrogen (MO-N) exhibits high lithium storage capacity (915mAhg−1 at 100mAg−1 for 50 cycles), great cycling stability (94.5% capacity retention versus the second cycle) and excellent rate capability (510mAhg−1 at 1000mAg−1). In particular, when cycling at a high current density of 1500mAg−1, the reversible capacity of the MO-N sample can still be maintained as high as 480mAhg−1 with a high capacity retention of 93.7% after 200 cycles. Even in a narrower voltage range of 0.01–1.5V, the lithium storage capacity of the MO-N sample can reach 556mAhg−1 at 100mAg−1 with a very good cycling stability (over 91% capacity retention from the second cycle) and have an excellent rate capability of 269mAhg−1 at 1000mAg−1. Both MO-N and MO-A samples present a very high volumetric capacity of 741.2mAhcm−3 and 647.4mAhcm−3 at 100mAg−1, respectively. Such high performances both in the voltage ranges of 0.01–3V and 0.01–1.5V are among the highest reported. Ex-situ SEM images showed clearly the excellent morphological and structural stability of our materials. The results demonstrate that the unique hierarchical mesoporous microspheres/carbon structure is favorable for improving the cyclability and rate capability in energy storage applications. Our effective synthesis strategy can be broadened to construct other mesoporous metal oxides/carbon composites for high-performance lithium ion batteries.