Thermal effect is a plateau that limits the output of high-power, high beam quality laser, and thermal effects become worse with the increase of pump power. We can reduce the effects caused by thermal effects from pumping, laser medium shape, cooling method and other aspects. In this article, by using finite element analysis software, the thermal effects between Nd:Glass and Nd:YAG laser crystal was analyzed and compared. The causes of generation for thermal effects, and factors that influence the distribution in laser medium were analyzed, including the light source, the laser medium shape and the working mode. Nd:Glass is more suitable for low repetition frequency, high energy pulsed laser output, due to its large size, line width and so on, and Nd:YAG is more suitable for continue or high repetition rate laser output, due to its higher thermal conductivity.