The electronic structure of CuIr$_2$S$_4$ has been investigated using various bulk-sensitive x-ray spectroscopic methods near the Ir $L_3$-edge: resonant inelastic x-ray scattering (RIXS), x-ray absorption spectroscopy in the partial fluorescence yield (PFY-XAS) mode, and resonant x-ray emission spectroscopy (RXES). A strong RIXS signal (0.75 eV) resulting from a charge-density-wave gap opening is observed below the metal-insulator transition temperature of 230 K. The resultant modification of electronic structure is consistent with the density functional theory prediction. In the spin- and charge- dimer disordered phase induced by x-ray irradiation below 50 K, we find that a broad peak around 0.4 eV appears in the RIXS spectrum.