In this paper, the ablation of fused silica by femtosecond laser burst mode and normal pulse mode was studied by three-dimensional two-temperature model and verified by experiments. The change of electron heat capacity, electron conductivity, reflectivity, and transmissivity of fused silica irradiated by femtosecond laser pulses were studied. The ablation crater shape was predicted and compared with experiments. The incubation effect induced by sub-pulses in a burst was investigated. It was found that when the sub-pulse separation time is 50 ns, the incubation effect of burst mode decreases with the increase of the number of sub-pulses, which is caused by the heat diffusion during time between sub-pulses. However, the incubation effect of burst mode increases with increase of sub-pulse number when the sub-pulse separation time is 1 ps. An optimal combination of sub-pulse number and sub-pulse separation time was found, in which the highest machining efficiency and the smallest thermal damage area could be obtained.