The thermal effect of LD end-pumped rectangular separated laser amplifying medium was analyzed and studied. Thermal conduction model of Cr,Yb:YAG/Yb:YAG composite structure was established. The temperature distribution inside the medium was calculated by utilizing the finite element method. The computing method of the medium refractive index vary with temperature was given, and worked out the output end face wave front phase distribution change with temperature. The results reveal that, while the pump power density is unchanged, with different pumping time the temperature distribution and refractive index at the direction of the optical section are different. With the increasing of the pumping time, the temperature and refractive index also increases, the output end face wave front phase distortion enlarge as well. While the pump power density increases, the variation tendency of temperature and refractive index are similar to the situation while the pumping time changes. The thermal effect becomes more serious as the growths of pumping time and the increases of pump power density.