Ultra-short pulsed laser ablation of crystalline silicon is characterized by a complicated heat diffusion process. In this research, a computational investigation is undertaken to achieve the temperature distribution and heat effect as a function of micromachining parameters. Heat accumulation and heat affected zone (HAZ) of silicon ablation by ultra-short lasers are estimated through solving coupled energy balance equations. The laser energy deposition and possible non-thermal ablation process are analyzed in the case of succession of laser pulses. Thermal-mechanical response induced by temperature gradient is discussed around the laser ablation region. The agreement between the model calculations and experimental results show that this research provides an efficient thermal analysis method, and a feasible way to optimize process parameters with minimum thermal damages.