Abstract Micro-Raman spectroscopy and method of Raman data calibration are proposed for the quantitative study of the proton-exchanged LiNbO3 channel waveguides, which contain the different HxLi1–xNbO3 phases, depending on the fabrication conditions. The spectroscopic parameters, phase composition and electro-optic properties of these waveguides have been found to be depending on the small variation of stoichiometry in the near-congruent lithium niobate substrates used for waveguides fabrication.