The thickness of the organic coating on the radome is directly related to the radar target positioning accuracy and tracking capabilities. Lock-in infrared non-destructive testing technology has the advantages of non-contact measurement and a large detection area, which can be used to detect and evaluate the thickness of the coating. This paper theoretically and numerically investigated the functional relationship between the thickness of the coating and the phase under thermal excitation at different frequencies, and analyzed the influence of loading frequency on thickness detection. Epoxy-coated/ceramic substrate samples were prepared, lock-in infrared experiments were conducted on coatings of different thicknesses, and a calibration curve was established. The results show that the average error of thickness measurement is within 5%, which has good practical value for engineering applications.