On the basis of the heat transfer, a three-dimensional heat conduction model was proposed. The coating applied sinusoidal variation of heat flux was analyzed using large-scale finite element analysis software ANSYS. The use of two loading and subtraction effectively overcome the effects brought about by the constant part and environmental factors. Then data fitting method for seeking phase was discussed. Changing loading frequency, multiple sets of the quantitative relationship curves were obtained. From the theoretical point of view, the relationship of the phase between the modulation frequency and thickness were revealed. Finally, using the linear stages in curves, the quantitative relationship between phase and thickness was identified. A theoretical basis for precise measurements of coating thickness using infrared lock-in method was provided.