The cross-section shape simulation model of micro-groove in femtosecond laser ablation of quartz glass was built based on the ablation rate model of transparent dielectric. Besides, the model was verified by ablation experiment. The effect of pulse energy and scan speed on the cross-section shape of micro-groove was analyzed to achieve the adjustment method of micro-groove shape. The analysis of simulation results shows that the depth and sidewall angle of micro-groove can be improved by decreasing the spot radius, increasing the pulse energy or slowing the scan speed. The width of micro-groove be improved by increasing the pulse energy or slowing the scan speed, but with the increasing of spot radius, it first increases and then decreases. The width of micro-groove reaches a maximum of 8.13 μm at the spot radius of 13 μm with the pulse of 4 μJ and the scan speed of 0.2 mm/s.