In the experiment of 10.6 μm continuous wave CO2 laser induced diffusion, the substrate is irradiated by a focused laser beam. To realize selective diffusion in local region, the diameter of the laser beam spot on the surface of the semiconductor substrate is only about dozens of microns. Because temperature rise of the exposed region must meet the requirement of diffusion experiment, high power density of the incident laser beam is necessary. On the other hand, the 10.6 μm light absorption coefficient of semiconductors such as Si, InP increases with the rising of temperature. The above two factors can easily lead to a thermal runaway phenomenon. The mechanism of thermal runaway was analyzed, then a numerical method was proposed to calculate the relation between the temperature of the exposed region and the power density of the incident laser beam. When the semiconductor substrate is kept at room temperature before the laser irradiation, it is shown that the temperature of the exposed region cannot be induced steadily to the value required in the diffusion experiment by using irradiation of laser beam with constant power. This problem can be avoided by preheating the substrate and real-time controlling the temperature of the exposed region.