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The formation and decay of high temperature phases in HxLi1−xNbO3 waveguide layers have been studied by means of waveguide mode spectroscopy and x-ray rocking curve measuring. The hydrogen doped layers with x ∼ 0.47 in (001) LiNbO3 were created by proton exchange reaction in melt benzoic acid. The high temperature phases were frozen by quenching from T = 200°C. It has been shown that these phases possess a 9% higher refractive index and 16% lower deformation in reference to the characteristic of HxLi1−xNbO3 phase equilibrium at room conditions. The relaxation of the high temperature phase to the equilibrium one has been traced at T = 100°C.