Thermal rectification refers to the phenomenon that heat fluxes or equivalent thermal conductivities are different under the same temperature difference when temperature gradient directions are different. The nature of the thermal rectification is that the structure has different effective thermal conductivities in different directions. Most of previous studies focused on thermal rectification of temperature-dependent thermal conductivity materials or variable cross section area structure, and the effect of thermal contact resistance at the interface was investigated very rarely. In the present paper we present the analytical and finite element numerical solution of temperature field and thermal rectification ratios of a composite structure with variable cross section area and thermal conductivity under different interface thermal contact resistances. The prescribed temperature boundary condition is introduced by penalty method, and the temperature jump condition at the interface is implemented by the definition of thermal contact resistance directly. The nonlinear heat conduction problem caused by temperature-dependent thermal conductivity and interface thermal contact resistance is then solved with a direct iteration scheme. Comparisons between experimental results and the present theoretical and numerical results show the feasibility of the proposed model. Then parameter investigations are also conducted to reveal the effect of some key geometric and material parameters. Numerical results show that thermal contact resistance plays an important role in the temperature field and thermal rectification ratio of the two-segment thermal rectifier. With the increase of the length ratio, thermal ratification ratio increases first and decreases then, and the optimal length ratio varies with both thermal contact resistance and cross-section radius change rate of the two segments. In general, the existence of thermal contact resistance can increase the total thermal resistance of the rectifier and magnify the distinction of the heat flux in forward and reverse cases. However, if the thermal contact resistance is too large, this distinction will decrease and correspondingly the thermal rectification ratio becomes low. With the increase of the boundary temperature difference, thermal rectification ratio increases due to the effect of temperature-dependent thermal conductivity. In the present study, we propose a theoretical and numerical approach to designing and optimizing the length ratio, cross-section radius change rate, thermal conductivity, boundary temperature difference and interface thermal contact resistance to obtain the maximal thermal rectification ratio of a bi-segment thermal rectifier, as well as the manipulation of thermal flux in engineering applications.