Nanostructured transition metal oxides have attracted considerable attentions for both high-capacity and high-rate, but great challenges remain to utilize them. In order to overcome these challenges, hierarchical three-dimensional CoMoO4/polypyrrole core-shell nanowire (NW) arrays on flexible and conductive carbon cloth (CC) have been successfully constructed through a facile two-step solution-based approach. The hybrid NWs electrode as a binder-free lithium ion batteries (LIBs) anode material exhibits a reversible capacity of around 1400–1450 mAh g−1 at a low current density of 100 mA g−1. The specific capacity retains at 753 mAh g−1 while featuring an excellent cycling properties with a capacity of 764 mAh g−1 after 1000 cycles under the current rate of 1200 mA g−1. Furthermore, full batteries have been fabricated and demonstrated characteristics of outstanding electrical stability and superior power output characteristics, which represents an efficient way for practical implementation.