Compounds with incommensurate structural modulations have been extensively studied in last several decades. However, the relationship between structurally incommensurate/commensurate phases and associated electronic states remains enigmatic. Here we report the coexisting of complex incommensurate structures and highly unusual electronic roughness on the surface of in situ cleaved IrTe2 by using scanning tunnelling microscopy/spectroscopy, corroborated with extensive density-functional theory calculations. This behaviour is traced to structural instability, which induces a structural transition from a trigonal to a triclinic lattice below transition temperature, giving rise to the formation of unidirectional structural modulations with distinct wavelengths, accompanied by the opening of a 'pseudo'-gap in the surface layer. With further cooling the surface adopts a structure that reflects an ~6 × periodicity that is different from the bulk 5 × periodicity. Calculations show that the structure distortion is not associated with a charge density wave, but is rather associated with Te p-electron bonding.