Background The recent studies have shown that visual performance might be affected by the ocular aberration after the corneal refractive surgery, and try to minimize it. This study was to investigate the effects of photorefractive keratectomy (PRK) and laser in situ keratomileusis (LASIK) on the higher order of wavefront aberration and analysis of their characteristics.Method This prospective study involved 32 eyes with similar refractive powers (-5.0 D to -6.0 D preoperatively). LASIK and PRK were performed with the same parameters of 6 mm diameter optical zone and 7 mm diameter transition zone ablation. Wavefront aberrations were tested using a ray tracing technique preoperatively and 3 months postoperatively.Three measurements were obtained for each condition; the root mean squared wavefront error (RMS), values for overall wavefront aberrations and each order of the Zernike aberrations were analyzed using the Matlab software. The 2-tailed t test was used for statistical analysis.Results Overall higher order aberrations were increased from (0.55±0.26) μm preoperatively to (0.93±0.37) μm for PRK and (0.79±0.38) μm for LASIK postoperatively. This was a 1.69 fold increase in the PRK group (t=3.95, P＜0.001)and a 1.43 fold increase in the LASIK group (t=2.60, P＜0.05). At 3 months, the mean RMS value for higher-order (3rd to 6th) were significantly increased compared with the corresponding preoperative values (P＜0.05). The fourth order aberrations, spherical like aberration, were dominant by a 2.64 fold in PRK and a 2.31 fold in LASIK. Different influences of the PRK group and LASIK group were shown in the various zernike components. The statistically significant differences were seen in C40, C4+4, C5+1, C5+3, C5+5 and C6+2 of the PRK group and C3-3, C40, C5-5, C5+5, C6-2 of the LASIK group, which represents a 7.42, 3.58, 9.21, 2.72 and 5.3 fold increases in PRK group, and 6.40, 10.80, 11.06, 3.47 and 6.09 fold increases in LASIK group, respectively. C3-3 in LASIK was higher and C5+1 and C5+3 were lower than those in the PRK group. C40 (spherical aberration) values were similar between PRK and LASIK, however, C3-1 and C31 (coma) in LASIK were higher than those in PRK, but these differences are of no statistical significance.Conclusions PRK and LASIK may increase ocular higher-order aberrations, but they both have their own features.The difference between the two types of surgery may be correlated with the change of the corneal shape, the conversion of biodynamics, the healing of the corneal cut, and re-structured corneal epithelium and/or the stroma.