The theoretical model of the thermal effects of the Tm:YAG laser which works at a low temperature by heating the rod ends of crystal was established. The temperature, stress and optical distortion of the crystal were simulated by the finite difference method. The simulation results show that, the designing of heating the crystal rod ends can reduce the maximum stress of crystal and minimize the stress damage accordingly. Although the complexity of the distribution of the temperature and stress caused by the crystal rod ends heating can cause a complex refractive index distribution, but it makes little effect on the light propagation because of the small changing refractive index value. The heating area is small and has no enough influence on the laser packaging.