Bacteriorhodopsin (BR) and halorhodopsin (HR) are well-known light-driven ion-pumping rhodopsins. BR transfers a proton from the intracellular medium to the extracellular medium. HR takes in chloride ion from the extracellular medium. A new light-driven sodium ion-pumping rhodopsin was discovered in 2013 by Inoue, Kandori, and co-workers (Nat. Commun. 2013, 4, 1678). The purpose of this article is to elucidate the proton, sodium ion and chloride ion transfer mechanisms and the geometrical changes of the intermediates. The absorption maxima of three rhodopsins were calculated by the SAC/SAC-CI method using the QM/MM optimized geometries. For BR, the SAC-CI results supported the previously proposed proton-transfer mechanism; (1) the photoisomerization from all-trans to 13-cis retinal (K intermediate), (2) the relaxation of the retinal structure (L intermediate), (3) the proton transfer from the Schiff base to the counterion residue (ASP85) (M intermediate), (4) the proton transfer from the ASP96 to the Schiff base (N intermediate), and (5) the thermal isomerization from 13-cis to all-trans retinal (O intermediate). The proton releases to the extracellular medium through the ASP96, the Schiff base, the ASP85, and the GLU204 or GLU194 from the intracellular medium. Furthermore, it clarified that the guanidine group rotation of ARG82 changes the excitation energies of the L and N intermediates, but the effect is small for the resting state and the K, M, and O intermediates. The theoretical calculations suggested that the ARG82 rotation occurs in the N intermediate from the comparison between the experimental absorption spectra and the theoretical excitation energies. For the KR2, the Kandori group proposed the sodium ion transfer mechanism; (1) the photoisomerization from all-trans to 13-cis retinal (K intermediate), (2) the relaxation of the retinal structure (L intermediate), (3) the proton transfer from the Schiff base to the counterion residue (ASP116) (M intermediate), (4) the sodium ion passes through the cavity formed by the rotation of the counterion residue (ASP116) (O intermediate) and (5) the proton of the ASP116 reassociates to the Schiff base. The steps (1) to (3) are the same as ones of BR The SAC-CI results supported the proposed sodium ion transfer mechanism and suggested that the sodium ion transfer proceeds in the O intermediate as follows; (1) the sodium ion connects with the Schiff base in the cavity formed by the ASP116 rotation, (2) at the same time that the sodium ion passes through the Schiff base, the Schiff base forms the hydrogen bond to the proton of ASP116, and (3) at the same time that the sodium ion transfers to the extracellular medium, the proton reassociates with the Schiff base from the ASP116. Furthermore, our results indicated that the retinal is not all-trans but 13-cis when the sodium ion passes through the Schiff base in the O intermediate. For the HR, since the counterion residue is replaced by the THR126, the proton dose not transfer from the Schiff base. Instead, the chloride ion transfers in the opposite direction to the proton of BR and the sodium ion of KR2. The SAC-CI results supported the previously proposed chloride ion transfer mechanism; (1) the photoisomerization from all-trans to 13-cis retinal (K intermediate), (2) the relaxation of the retinal structure (L intermediate), (3) the chloride ion passes through the Schiff base from the extracellular medium side to the intracellular medium side (N intermediate) and (4) the chloride ion transfer from the Schiff base to the intracellular medium and the thermal isomerization from 13-cis to all-trans retinal (O intermediate). Furthermore, our results suggested that the Schiff base forms bonds to the hydroxide ion instead of the chloride ion in the O intermediate. The negative ion is necessary to keep the total charge around the Schiff base in the O intermediate.