A three-dimensionally aligned CNT/Si hybrid for flexible and efficient anode has been developed for lithium ion batteries. A delithiation capacity of 2562 mA h g⁻¹ was achieved at a current density of 1 A g⁻¹ with 93% retention after 100 cycles, and the delithiation capacity was retained at 1055 mA h g⁻¹ after 1000 cycles at 5 A g⁻¹. The high specific capacity, cyclic stability and rate performance are ascribed to the aligned CNTs that serve as both conductive pathways and buffer scaffolds to effectively accommodate the volume change of Si in three dimensions. In addition, a stable electrochemical performance is maintained after increasing the areal density of the hybrid anode by over 10 times, indicating great promise for practical applications.