Provided are a carbon nanotube structure more excellent in electric conductivity, thermal conductivity, and mechanical strength, and a method of manufacturing the carbon nanotube structure. A carbon nanotube composite structure is characterized by including: a first carbon nanotube structure in which functional groups bonded to plural carbon nanotubes are chemically bonded and mutually cross-linked to construct a network structure; and a second carbon nanotube structure in which functional groups bonded to plural carbon nanotubes are chemically bonded and mutually cross-linked to construct a network structure, the second carbon nanotube structure being combined with the network structure of the first carbon nanotube structure.