In order to realize the precisely thinning of flute on the surface of quartz by femtosecond laser, the line-surface ablation process means are taken to study the effects of the pulse energy on the ablation morphology of groove, and the ablation experimental research of flute with different line overlap rates δ are carried out. The laser scanning confocal microscope is used to observe and analyze the depth, bottom surface roughness and other morphology features of flute. The results show that when the line overlap rate δ satisfies 40%≤ δ ≤80%, with the increase of δ, the depth and sidewall angle of flute decrease, when δ is 40%, the depth, width and sidewall angle of groove is 14.56 μm, 261.8 μm and 59.1°, respectively. The bottom surface roughness decreases as well, when δ is 80%, Ra and Rz reach the minimum of 0.19 μm and 1.23 μm, respectively. The profile fluctuation parallel to scanning speed increases at first then decreases, when δ =80%, Ra′ ≈Ra, Rz′ ≈Rz; The root mean square of bottom surface Sq decreases with the increase of δ, Sq reaches the minimum of 0.16 μm when δ is 80%.