Carbon nanotube films (CNT-1 and CNT-2) were fabricated in a vertical CVD gas flow reactor with water sealing. CNT-1 films consist of ordered crystalline carbon nanotubes, while CNT-2 are defective carbon nanotube films. The films are flexible and transferrable and can be used as binder-free anodes for lithium-ion batteries (LIB). Electrochemical measurements show that CNT-2 possess a reversible capacity of 452 mA h g−1 under a current density of 30 mA g−1, which is higher than that of CNT-1 (375 mA h g−1) under the same current density. In addition, the CNT-2 shows a reversible capacity of 107.9 mA h g−1 after 500 cycles at a current density of 3000 mA g−1, while 82.1 mA h g−1 for CNT-1 under the same condition. Good correlations between morphological factors, defective structure and electrochemical performance are observed.