To evaluate the regional effects of different corneal cross-linking (CXL) protocols on corneal biomechanical properties., The study involved both eyes of 50 rabbits, and the left eyes were randomized to the five intervention groups, which included the standard CXL group (SCXL), which was exposed to 3-mW/cm2 irradiation, and three accelerated CXL groups (ACXL1-3), which were exposed to ultraviolet-A at irradiations of 9 mW/cm2, 18 mW/cm2, and 30 mW/cm2, respectively, but with the same total dose (5.4 J/cm2). A control (CO) group was not exposed to ultraviolet-A. No surgery was done on the contralateral eyes. The corneas of each group were evaluated by the effective elastic modulus (Eeff) and the hydraulic conductivity (K) within a 7.5-mm radius using nanoindentation measurements., Compared with the CO group, Eeff (in regions with radii of 0-1.5 mm, 1.5-3.0 mm, and 3.0-4.5 mm) significantly increased by 309%, 276%, and 226%, respectively, with SCXL; by 222%, 209%, and 173%, respectively, with ACXL1; by 111%, 109%, and 94%, respectively, with ACXL2; and by 59%, 41%, and 37%, respectively, with ACXL3 (all P < 0.05). K was also significantly reduced by 84%, 81%, and 78%, respectively, with SCXL; by 75%, 74%, and 70%, respectively, with ACXL1; by 64%, 62%, and 61%, respectively, with ACXL2; and by 33%, 36%, and 32%, respectively, with ACXL3 (all P < 0.05). For the other regions(with radii between 4.5 and 7.5 mm), the SCXL and ACXL1 groups (but not the ACXL2 and ACXL3 groups) still showed significant changes in Eeff and K., CXL had a significant effect on corneal biomechanics in both standard and accelerated procedures that may go beyond the irradiated area. The effect of CXL in stiffening the tissue and reducing permeability consistently decreased with reducing the irradiance duration.