Scleral collagen cross-linking (SXL) is one of the most promising treatments to control the pathologic process of myopia. The exact procedure and effects on myopic animal models still need to be explored. We applied an iontophoresis-assisted delivery system to the riboflavin/ultraviolet A (UVA) SXL procedure, and conducted an accelerated UVA irradiation (10 mW/cm2, 9 minutes) on a myopic animal model to explore the effects on scleral biomechanical properties and collagen metabolism. By form deprivation, ninety-six New Zealand white rabbits developed relatively stable myopia and then underwent the SXL surgery or sham-operation. All the sample and statistics were obtained from 4 time points (1-day, 10-day, 1-month and 3-month) after the surgery. The results show that the ultimate stress, Young's modulus and physiological Young's modulus of treated myopic sclera were significantly increased compared with those of untreated ones in all four groups. In addition, there were significant differences in the expression of genes and proteins related to collagen metabolism between the treated sclera samples and untreated ones. It demonstrated that iontophoresis-assisted accelerated Riboflavin/UVA SXL might be a potential method to control the pathological process of myopia.