The invention provides a super high-rise tower structural system of hexagonal barrels arranged in a honeycomb-shaped cluster. According to a honeycomb structure, a plurality of structural units of giant hexagonal barrels are combined in a cluster mode; and along with the increase of the height of a building, the number of the structural units of the giant hexagonal barrels is gradually reduced, and a novel pagoda-shaped super high-rise structural system is formed. A hexagonal barrel structure composed of giant hexagonal concrete filled steel tubular columns and grilling tubular type double steel plate concrete shear walls is adopted inside the super high-rise tower structural system, and the giant vertical load and the giant horizontal load of the super high-rise building are borne; and a frame tube structure composed of giant hexagonal concrete filled steel tubular columns and giant oblique supporting frames is adopted outside the super high-rise tower structural system, and the requirement for natural lighting of the super high-rise building can be met. The super high-rise tower structural system of the hexagonal barrels arranged in the honeycomb-shaped cluster has the advantages of large structural rigidity, rich facade shape, simplicity, stability, good wind stability performance, good anti-seismic capability, convenient construction and the like, and a super high-rise building structure over one thousand meters can be built.