The magnetism of Kitaev materials has been widely studied, but their charge properties and the coupling to other degrees of freedom are less known. Here we investigate the charge states of α-RuCl3, a promising Kitaev quantum spin liquid candidate, in proximity to graphite. We discover that few-layered α-RuCl3 experiences a clear modulation of charge states, where a Mott-insulator to weak charge-transfer-insulator transition in the 2D limit occurs by means of heterointerfacial polarization. More notably, distinct signals of incommensurate charge and lattice super-modulations, regarded as an unconventional charge order, accompanied in the insulator. Our theoretical calculations have reproduced the incommensurate charge order by taking into account the antiferroelectricity of α-RuCl3 that is driven by dipole order in the internal electric fields. The findings imply that there is strong coupling between the charge, spin, and lattice degrees of freedom in layered α-RuCl3 in the heterostructure, which offers an opportunity to electrically access and tune its magnetic interactions inside the Kitaev compounds.