Femtosecond laser processing has been extensively used in micromachining, especially for the precision processing of hard and brittle materials. However, the precision of the materials ablated by femtosecond laser is not easy to control. This paper reports an experimental and theoretical study on the ablation characteristics of fused silica using high repetition rate femtosecond laser. An experimental study of microchannels milling on the fused silica was carried out. The influence of pulse energy, repetition rate, scanning velocity, scanning times on the size and morphology of the microchannels was obtained. Simultaneously, the experimental data on the depth and width of microchannels under different parameter combinations were acquired through the orthogonal experiment. The prediction model of aspect ratio was obtained by BP neural network algorithm. Finally, the verification test was established and showed that the experimental results were consistent with the theoretical results. It would provide a theoretical basis for further study on the microchannels fabrication of femtosecond laser.