This work is devoted to the study of the drift of the operating point of integrated-optical circuits based on proton-exchange waveguides in lithium niobate crystal with a recovered structure of the near-surface layer. Recovered of the damaged near-surface layer of lithium niobate wafer was carried out using pre-annealing at temperature of 500 °C. Drift of operating point is characterized by a constant change in the optical output power of the integrated-optical circuits when a bias voltage is applied to the electrodes or temperature changes. Recovered of the damaged near-surface layer of lithium niobate wafer leads to a decrease in the short-term and long-term drifts of the operating point of integrated-optical circuits. Crystal structure factor was investigated on the drift of operating point of integrated-optical circuits based on lithium niobate crystal.