This work involves results of research on short-term and long-term DC-drifts in electro-optical modulators based on annealed proton exchange waveguides in LiNbO3 crystals after wafer pre-annealing. The relaxation time of the DC-drift of the operating point for a short-term drift is minutes, and for a long-term drift, hours and days. DC-drift was measured by applying bias voltage and changing crystal temperature. Obtained results shows significant impact on stability of operating point in EO-modulators after treatment of defective structure of the near-surface layer of a LiNbO3 crystal. Treatment of the disturbed near-surface layer of a LiNbO3 crystal results in twice reduction of short-term DC-drift and increase of operation stability of electro-optical modulators during long-term measurement of temperature by activation energy calculation.