Purpose: To report the 3 year efficacy and predictors of transepithelial corneal cross-linking assisted by iontophoresis (I-CXL) for 10 min using the least absolute shrinkage and selection operator (LASSO) regression in Chinese patients with progressive keratoconus.Methods: This retrospective study included 30 eyes of 25 patients, of mean age 18.48 ± 4.02 years (range: 11 to 28 years). All patients underwent stromal imbibition of riboflavin solution for iontophoresis for 10 min, followed by epithelium-on CXL. The uncorrected distance visual acuity (UDVA; in logarithm of the minimum angle of resolution [LogMAR] units), corrected distance visual acuity (CDVA; in LogMAR units), spherical equivalent (SE); max keratometry (Kmax); minimum corneal thickness (MCT); the index of surface variance (ISV); the index of vertical asymmetry (IVA); the keratoconus index (KI); the center keratoconus index (CKI); and the index of height decentration (IHD), corneal optical coherence tomography (OCT), and confocal microscopy were evaluated at baseline and postoperatively at 1, 3, 6, 12, 24, and 36 months. Predictors of changes in CDVA and Kmax 3-year postoperatively compared with baseline were analyzed using the LASSO regression with internal tenfold cross-validation, as indicated by average root mean squared error (RMSE) and R-squared (R2) values.Results: Corneal OCT at 1 month detected the demarcation line in 24 eyes (80%), at a mean depth of 238.97 ± 53.69 μm. Average CDVA improved from 0.26 ± 0.17 LogMAR at baseline to 0.19 ± 0.13 LogMAR at 3 years (P < 0.05), average Kmax decreased from 59.72 ± 8.71 diopters (D) at baseline to 58.03 ± 7.96 D at 3 years (Delta: −1.68 ± 3.15 D, P < 0.05). ISV, IVA, KI, and IHD also decreased significantly. After LASSO regression for predictor selection, ten parameters (age, gender, baseline UDVA, CDVA, SE, MCT, ISV, IVA, KI, and IHD) were the predictors of CDVA changes 3 years after I-CXL (RMSE = 0.0054; R2 = 0.89). Age, baseline MCT, KI, and CKI value were associated with Kmax changes (RMSE = 7.3828; R2 = 0.57).Conclusions: I-CXL for 10 min is safe and effective in patients with keratoconus, with good 3 year outcomes and the symmetry indices could predict the improvement of CDVA at 3 year after I-CXL.