Effects of wavelength-selective infrared irradiations to nematic and smectic phases on the domain structures were investigated using a free electron laser (FEL) system for a rod-like mesogen possessing a lateral C=O group which exhibits nematic, smectic A and smectic C phases. Them mesogen molecules tend to spontaneously align in a homeotropic way on BaF2 substrate. It was observed that the infrared irradiation of a pulsed laser whose wavelength corresponds to that of a C=O stretching absorption band (5.83 pm) induces transient turbulence of the liquid crystalline domains. This transient turbulence was recovered to the original homeotropic alignment soon after the termination of irradiation. Some results strongly indicated that these phenomena are induced by the thermodynamically non-equilibrium state generated by infrared laser pulse irradiation. These observations. imply that the domains as well as the collective modes of mesophase could be modified by infrared pulse irradiations with an appropriate power, whose wavelength corresponds to the vibrational band of a specific chemical bond.