Scleral collagen cross-linking is one of the most promising treatments to control the pathologic process of myopia. However, the exact procedure and its impact on animal models of myopia are still to be explored. We modified the scleral riboflavin/ultraviolet A (UVA) cross-linking procedure with an iontophoresis-assisted drug delivery system and an accelerated UVA irradiation (10 mW/cm2, 9 min) and applied this treatment to an animal model of myopia. Ninety-six New Zealand White rabbits developed relatively stable myopia by visual deprivation and then underwent the modified scleral cross-linking surgery. All the statistics and sample collection were obtained from 4 postoperative time points (1-day, 10-day, 1-month and 3-month groups). We found that the ultimate stress, Young's modulus and physiological Young's modulus of treated myopia sclera were significantly increased and maintained in 4 groups. The abnormal elongation of the myopic eye was effectively controlled 1 month after the treatment and even almost halted 3 months after the treatment. The histochemical assay revealed no notable post-surgery damage or apoptosis in the retina and choroid. Vigorous collagen synthesis was observed in scleral fibroblasts of the treated samples but were rarely observed in the untreated ones under electron microscopy. Furthermore, the remarkable difference in collagen gene expression and protein content between treated and untreated samples also indicated that an alteration in collagen metabolism may be triggered by the treatment. The effectiveness and safety exploration suggested that the modified scleral cross-linking procedure may be a potential method to control the pathologic process of myopia.