MnO, with low operation potential and cost, is very attractive among transition metal oxides as an anode material for Li ion batteries. In this work, hierarchical MnO@C nanorods, in which ultra-small MnO nanocrystals (generally <5 nm) were homogeneously dispersed in a carbon matrix and further coated with a well-proportioned carbon shell, were prepared through a two-step hydrothermal treatment and subsequent sintering at 600 °C, with a slow heating rate of 5 °C min−1. In contrast, when sintered at a higher temperature (800 °C) and a faster heating rate (10 °C min−1), the ultra-small MnO nanocrystals agglomerated into nanoparticles (30–80 nm) and partially lost the contact with the outer carbon shell. Profiting from the highly-dispersed ultra-small nanocrystals in the carbon matrix and the well-proportioned carbon shell, the carbon-coated MnO nanocrystals exhibited a reversible capacity of 481 mA h g−1 after 50 cycles at a current density of 200 mA g−1, which is higher than that of carbon-coated MnO nanoparticles. The results disclose the important roles of small particles and carbon shells in developing advanced anode materials for Li ion batteries.