MnO is one of the most attractive anode materials for Li ion batteries (LIBs) due to its high theoretical capacity and low voltage hysteresis. However, its inherent low conductivity and large volume expansion hinder real application. Herein, we construct a flexible freestanding film of MnO quantum dots, N-doped carbon layer and carbon nanotubes by an effective method and demonstrate its direct application as an anode for LIBs. The microstructure observations reveal that well-dispersed MnO quantum dots with the average of 2–5 nm attach tightly on highly conductive carbon nanotube substrates and covered by N-doped carbon layers. Such unique nanocomposite structure provides effective carbon protective layers to accommodate volume change, ensure almost the whole surface of each MnO quantum dots to attend electrochemical reaction, and increases electron conductivity and reduces Li+ diffusion distance. Furthermore, kinetic analysis and characterization tests indicate that capacitive contribution for Li storage in the freestanding film is calculated to be high and further oxidation of Mn2+ to higher valence state upon cycling generates lots of specific capacity, thus endowing it with excellent rate, ultrahigh capacity and outstanding cycling stability. The flexible freestanding anode delivers ultrahigh capacity of 1741mAh g−1 after 120 cycles at 0.1 A g−1, a high-rate capability of 858 mAh g−1 at 3.2 A g−1 after 120 cycles at 0.1 A g−1, and long-term cycling stability with a capacity of 136.5% at 1.0 A g−1 after 1000 cycles. The unique nanostructure design is believed to have great potential in general synthesis of the composite consisted of CNT and oxide quantum dots for energy storage.