The thermal effect of the laser diode end-pumped rectangular separated amplifier was studied. Thermal conduction model of Cr,Yb∶YAG/Yb∶YAG composite structure accord with reality was established. In the separated amplified structure, the internal temperature field variation of amplifier under different gain media and cladding structure was analyzed. The temperature distribution inside the material was calculated quantitatively, and the phase distribution of the wave front with the change of temperature was given. The research shows that in the thinner cladding thickness and smaller thickness ratio, medium face has a higher temperature rise, and aggravated thermal effect; the thermal effect of the amplifier is weaken by relative more thick cladding and larger thickness ratio. The research results can provide theoretical guidance to depress the thermal effect of composite structure amplifier.