In this paper, a perturbation theory of thermal rectification is developed for a thermal system where an effective thermal conductivity throughout the system can be identified and changes smoothly and slightly. This theory provides an analytical formula of the thermal rectification ratio with rigorous mathematical derivations and physical assumptions. The physical meanings and limitations of the present theory are discussed in detail. Furthermore, a physical relationship among the thermal rectification, system length, temperature difference, and thermal conductivity is built. It reveals the linear relationship between the thermal rectification ratio and temperature difference. Also, the size dependence of the thermal rectification relies on the specific form of the thermal conductivity. In addition, several previous experimental and numerical observations are well explained by this theory.