The paper considers the issue of pulse laser heating of double-layer system in which the first layer is transparent relative to the actuating flow and the second is a highly lossy one. Temperature profiles of heating double-layer system at different lengths of actuating pulse have been obtained by the numerical simulation technique. It was shown that heating maximum position does not conform to medium interface. The results obtained were used when analyzing the process of laser separation of gallium nitride crystal from sapphire substrate.