Objective To investigate the improvement in visual quality in high myopia patients after sub-Bowman′s keratomileusis (SBK) using femtosecond laser or a mechanically guided system using Q values. Methods In this prospective study, 110 cases (220 eyes) of high myopia patients were treated and screened in our department from June 2013 to January 2015. They were divided into an OUP group and a Femto group randomly. Fifty-five high myopia patients (110 eyes) in the Femto group were treated with SBK using femtosecond laser to create corneal flaps guided by the Q value, and the same number of high myopia patients in the OUP group were treated with SBK using femtosecond laser alone to create corneal flaps. Visual acuity, corneal flap thickness, residual refractive error, total higher-order aberrations, spherical aberration, horizontal coma, vertical coma, and contrast sensitivity were evaluated during the follow-up. t-tests and repeated measures analysis of variance were used for data analysis in the first day, the first week, the first month, the third month, and the sixth month after SBK. Results There were no statistically significant differences between the two groups for visual acuity, residual refractive error, vertical coma, or contrast sensitivity(P>0.05), but results for patients in the Femto group were better than results in the OUP group for corneal flap thickness and default (t=24.45, P＜0.01). In addition, the added values of total higher-order aberrations,spherical aberration and horizontal coma in patients in the Femto group were better than those in the OUP group(t=12.87, 7.12, 7.26, P＜0.01). Conclusion Aberrations from femtosecond laser flap SBK surgery for high myopia are milder and the procedure can provide relatively better visual quality.