We had investigated the electromechanical coupling coefficient (K2) of surface acoustic wave (SAW) on proton-exchanged (PE) and annealed PE (APE) z-cut LiNbO3 waveguides using octanoic acid. The penetration depth of hydrogen assumed to be equal to the waveguide depth (d) was measured by secondary-ion mass spectrometry (SIMS). The frequency response of SAW was measured with a network analyzer. The annealing process was carried out in a horizontal furnace kept at 400°C for 2 h under a dry O2 gas flow. The change of K2 in PE and APE samples fabricated under different conditions was dependent on kd, where k was the wavenumber. The experimental results showed that the variation of K2 in PE samples was significantly decreased with the increase of kd. The reduction of K2 may be due to the reduced piezoelectric coefficients in the PE layer. On the other hand, the variation of K2 in APE samples also exhibited the decreased tendency after annealing. It indicated that the annealing process could not restore the reduction of K2 caused by the PE process.