The disclosed method of manufacturing carbon nanotubes includes the steps of growing CNTs on a substrate 12 and cleaning the inside of a growth furnace 13 by supplying a cleaning gas that contains water into the growth furnace 13. In the cleaning step, the cleaning is performed such that 0.7≦(2[CO2]+[CO])/[H2]≦1.3 is satisfied, where [H2], [CO2], and [CO] denote the concentrations of hydrogen, carbon dioxide, and carbon monoxide, respectively, in a gas within the growth furnace 13.