Objective To assess and compare the morphology of laser in situ keratomileusis (LASIK) flaps created by Intralase FS60 femtosecond laser and the Moria M2 microkeratome. Methods 199 patients were evaluated and 200 eyes in Intralase group and 198 eyes in the microkeratome group. The RTVue optical coherence tomography (OCT) device was used to measure the morphology of LASIK flaps one week postoperatively. Nominal flap thickness was 110 μm for all four FS systems. Results The flaps in the Intralase group were regular and uniform, showing an almost planar configuration, and the difference of flap thicknesses in the horizontal and vertical meridians was not significant (t＝1.582, P＝0.114). The flaps created with the Moria M2 microkeratome were thinnest in the central zone. Thickness increased towards the periphery, resulting in a meniscus shape. The difference of flap thicknesses in the horizontal and vertical meridians was not significant (t＝1.010, P＝0.313). The mean deviation between the achieved and attempted flap thickness was smaller in the Intralase group (7.15±4.89) μm than that in the Moria M2 group (18.97±11.56) μm (P<0.01). Conclusions The morphologies of flaps created by Intalase femtosecond laser are more uniform and accurate than those created by the Moria M2 microkeratome.