Owing to their high reactivity toward lithium, molybdenum oxides have been widely studied as anode materials for lithium-ion batteries. The two most common molybdenum oxides, MoO₂ and MoO₃, are reported to undergo sequential insertion and conversion reactions during lithiation. Accordingly, the theoretical capacity of MoO₃ is higher than that of MoO₂ because of the higher oxidation state of Mo. However, some nanostructured MoO₂ exhibits abnormally high reversible capacity close to that of MoO₃, which cannot be explained by the conversion reaction mechanism. Herein, the charge storage behavior of the two molybdenum oxides is comparatively analyzed. Structural investigation using synchrotron X-rays demonstrates that the conversion reaction occurs in MoO₃, whereas MoO₂ accommodates a large amount of lithium in the form of metallic lithium. As a result, MoO₂- and MoO₃-based composite materials exhibit similar reversible capacities of ∼1017 and 1110 mA h g⁻¹, although the changes in the oxidation state of Mo during lithiation are much smaller in the MoO₂/graphene composite. First-principles calculations demonstrate that the origin of the different electrochemical properties is the different metal–oxygen bonding properties of MoO₂ and MoO₃. Understanding the bonding-dependent electrochemical properties in this work could provide a new perspective for designing high-performance electrode materials.