Hydrogen bonding in methanol clusters has been investigated by using inner-shell photoabsorption spectroscopy and density functional theory (DFT) calculations in the carbon and oxygen K-edge regions. The partial-ion-yield (PIY) curves of H(CH3OH)n+ were measured as the soft X-ray absorption spectra of methanol clusters. The first resonance peak in the PIY curves, which is assigned to the σ*(O–H) resonance transition, exhibits a 1.20-eV blue-shift relative to the total-ion-yield (TIY) curves of molecular methanol in the oxygen K-edge region, while it exhibits a shift of only 0.25 eV in the carbon K-edge region. Decreased intensities of the transitions to higher Rydberg orbitals were observed in the PIY curves of the clusters. The drastic change in the σ*(O–H) resonance transition is interpreted by the change in the character of the σ*(O–H) molecular orbital at the H-donating OH site due to the hydrogen-bonding (HB) interaction.