Entanglement of charge orderings and other electronic orders such as superconductivity is in the core of challenging physics issues of complex materials including high temperature superconductivity. Here, we report on the observation of a unique nanometer scale honeycomb charge ordering of the cleaved IrTe2 surface, which hosts a superconducting state. IrTe2 was recently established to exhibit an intriguing cascade of stripe charge orders. The stripe phases coexist with a hexagonal phase, which is formed locally and falls into a superconducting state below 3 K. The atomic and electronic structures of the honeycomb and hexagon pattern of this phase are consistent with the charge order nature, but the superconductivity does not survive on neighboring stripe charge order domains. The present work provides an intriguing physics issue and a new direction of functionalization for two-dimensional materials.