Objective  To compare the corneal topography of patients with myopia and astigmatism 3 months after femtosecond lenticule extraction （Flex） and femtosecond laser in situ keratomileusis （FS-LASIK）. Methods  In this prospective study， 323 myopic eyes of 165 patients with astigmatism who underwent Flex or FS-LASIK from January to September in 2013 in Beijing Tongren Hospital were examined. An independent samples t test was used to compare visual acuity， refraction and corneal topography measurements 3 months after surgery. Results  Three months after surgery， uncorrected visual acuities （UCVA） of logMAR in Flex and FS-LASIK were -0.10±0.08 and -0.11±0.10 and best corrected visual acuities （BCVA） were -0.11±0.07 and -0.12±0.07. These measurements were better than the BCVAs before surgery， which were -0.07±0.03 and -0.07±0.04 （t=4.083， 5.594 and 3.458， 6.440， P<0.01）. No significant difference in postoperative UCVA was seen between Flex and FS-LASIK （t=-0.811， -1.864， P＞0.05）. The cutting decentration with Flex （0.29±0.17 mm） was smaller than with FS-LASIK （0.40±0.17 mm）， respectively （t=5.662， P＜0.01）. There was no correlation with spherical equivalent （SE） in Flex （r=0.122， P＞0.05）， but there was a positive correlation with SE in FS-LASIK （r=0.210， P<0.01）. The postoperative surface regularity index （SRI） of Flex was higher than that of FS-LASIK， 0.34±0.25 and 0.22±0.21， respectively （t=-4.627， P＜0.01）. Conclusion  The cutting decentration of Flex is smaller than that of FS-LASIK， however the regularity of the corneal surface after FS-LASIK is better than that of Flex. Both techniques result in satisfactory visual acuity.