AIM: To compare the clinical and microstructural changes induced by different transepithelial iontophoresis-assisted corneal cross-linking (I-CXL) methods for keratoconus. METHODS: A total of 42 eyes of 42 patients with progressive keratoconus were divided into two groups. Group A received I-CXL for 5min, while group B received I-CXL for 10min. Visual acuity, optical coherence tomography (OCT), specular microscopy and confocal microscopy were evaluated preoperatively and at 1, 3, 6, and 12mo postoperatively. RESULTS: Twelve months after the operation, uncorrected visual acuity (UCVA) and corrected distance visual acuity (CDVA) were improved in both groups, with a better outcome in the I-CXL 10min group (P=0.025, 0.021, respectively). Kmax values decreased by 0.94±3.00 D in the I-CXL 10min group (P=0.033) but increased by 1.87±3.29 D in the I-CXL 5min group (P=0.012). OCT scans showed that the demarcation line was most visible and substantially deeper in the I-CXL 10min group. Confocal microscopy showed greater anterior stromal keratocyte decreases in the I-CXL 10min group than in the I-CXL 5min group at 3 and 6mo postoperatively (P<0.001); however, anterior stromal keratocytes and subbasal nerve density were not significantly different between the two groups at 12mo postoperatively. CONCLUSION: I-CXL for 10min more effectively halts the progression of keratoconus than I-CXL for 5min after 12mo of follow-up. However, long-term studies are needed to evaluate the efficacy and safety of I-CXL.