To investigate the effects of corneal thickness distribution and apex position on postoperative refractive status after full-bed deep anterior lamellar keratoplasty (FBDALK). This is a retrospective analysis of patients who were diagnosed with advanced keratoconus between 2011 and 2014 in our hospital. The base of the cone in all patients did not exceed the central cornea at a 6-mm range. The FBDALK was performed by a same surgeon. All patients had a complete corneal suture removal and the follow-up records were intact. Patients who had graft-bed misalignment or who were complicated with a cataract or glaucoma were excluded. Uncorrected visual acuity (UCVA), best spectacle corrected visual acuity (BSCVA), and Pentacam examination data were recorded at two years postoperatively. The recorded data included the superior-inferior (S-I) and nasal-temporal (N-T) corneal thickness differences in 2, 4, 6, and 8 mm diameter concentric circles with the corneal apex as the center (S-I2 mm, S-I4 mm, S-I6 mm, S-I8 mm, N-T2 mm, N-T4 mm, N-T6 mm, and N-T8 mm), the linear, X-axis, and Y-axis distance between the corneal pupillary center and the cornea apex, total corneal astigmatism at a zone of 3 mm diameter from the corneal apex (TA3 mm), the astigmatic vector values J0 and J45, and the corneal total higher-order aberration for 3 and 6 mm pupil diameters (HOA3 mm and HOA6 mm). Statistical analysis was performed by SPSS 15.0. A total of 47 eyes of 46 patients met the criteria and were included in this study. The mean follow-up time was (28±7) months. The mean UCVA was 0.45±0.23 (logMAR) (MAR: minimum angle of resolution) and the mean BSCVA was 0.19±0.15 (logMAR), which were all significantly positively correlated with postoperative TA3 mm and HOA3 mm. The mean S-I corneal thickness differences were (44.62±37.74) μm, and the mean N-T was (38.57±32.29) μm. S-I2 mm was significantly positively correlated with J0 (r=0.31), J45 (r=0.42), HOA3 mm (r=0.37), and HOA6 mm (r=0.48). S-I4 mm and S-I8 mm were significantly positively correlated with HOA3 mm (r=0.30, r=0.40) and HOA6 mm (r=0.46, r=0.35). The X-axis distance between corneal pupillary center and corneal apex was significantly positively correlated with J45 (r=0.29). In patients with advanced keratoconus after FBDALK, the unevenly distributed thickness at corneal pupillary area and the misalignment of corneal apex and pupillary center might cause significant regular and irregular astigmatism, which affected the postoperative visual quality.