Abstract: In order to study the nonuniform temperature rise and thermal effect in the Yb:YAG crystal, based on the theory of semi-analytical thermal analysis and working characteristic analysis of Yb:YAG microchip with super-Gaussian beam end-pumping and back-face cooling, a new solution of heat conduction equation was introduced and the general expressions of temperature field, thermal distortion field and additional optical path differences (OPD) of Yb:YAG microchip were obtained respectively. Some factors affecting the temperature distribution and thermal distortion of Yb:YAG microchip, such as the super-Gaussian beam with different orders,different spot radius, were quantitatively analyzed. If a Yb:YAG microchip with 0.08 atom fraction of ytterbium is end-pumped by the fifth order super-Gaussian beam with power of 50W in 300μm radius, its maximal temperature raise was up to 52.18℃ and its maximum thermal distortion was 0.1195μm and maximum additional OPD was 0.2152μm. The results can provide theoretical instruction for the heat insensitivity cavity design of microchip laser.