Background The purpose of this study was to compare the astigmatic correction by vector analysis in patients with high myopic astigmatism after femtosecond laser-assisted laser in situ keratomileusis (FS-LASIK) with cyclotorsion compensation or small-incision lenticule extraction (SMILE) with stringent head positioning. Setting Beijing Aier-Intech Eye Hospital, Beijing, China. Design A retrospective case series. Methods Patients who had correction of myopic astigmatism of 2 diopters (D) or more treated with either FS-LASIK with cyclotorsion compensation or SMILE with stringent head positioning were included. The results of vision and refraction were analyzed and compared between groups with the right eye. Results The study enrolled 94 patients (41eyes in an FS-LASIK with compensation of cyclotorsion group and 53 eyes in a SMILE with stringent head positioning control group. The mean preoperative manifest cylinder was -2.65 +/- 0.77D in the FS-LASIK group and 2.51 +/- 0.56D in the SMILE group (P = 0.302). At 12 months, there was no significant between-group difference in uncorrected distance visual acuity (UDVA, P = 0.274) and postoperative spherical equivalent (SEQ) (P = 0.107). 46.3% and 24.5% of eyes in the FS-LASIK and SMILE groups were within 0.25 D were within 0.25D postoperative cylinder, respectively, and 78% and 66% of eyes in these two groups were within 0.5 D postoperative cylinder (P = 0.027, P = 0.202). The vector analysis showed comparable between-group target-induced astigmatism (TIA) (P = 0.114), surgically induced astigmatism (SIA) (P = 0.057), difference vector (DV, P = 0.069), and the angle of error (AE) (P = 0 .213) values. The index of success (IOS) was 0.18 in the FS-LASIK group and 0.24 in the SMILE group (P = 0.024), with a significant difference between the two groups. Conclusion FS-LASIK with compensation of cyclotorsion showed a favorable correction of high myopic astigmatism (>= 2.0 D) compared to SMILE with stringent head positioning at 12 months.