Secondary glaucoma constitutes major sight-threatening complication of pediatric cataract surgery, yet the etiology remains unclear. The purpose of this study was to investigate the long-term anterior segment configuration and the association with secondary glaucoma in pediatric pseudophakia. Ultrasound biomicroscopy (UBM) was performed on 40 eyes of 26 children underwent pediatric cataract surgery and intraocular lens (IOL) implantation. The anterior chamber depth (ACD), angle-opening distance at 500 μm (AOD500), trabecular-iris angle (TIA), central corneal thickness (CCT), structural abnormities, IOL position, IOP, and incidence of glaucoma were evaluated. High insertion of iris, in which the iris root is attached more anteriorly than normal, was seen in 13 eyes (32.50%). IOL was located in the capsular bag in 19 eyes and in the ciliary sulcus in 21 eyes. Logistic regression analysis identified high insertion of iris (OR 3.40, 95% CI 1.03-11.17, p = 0.03) and IOL implantation in sulcus (OR 1.39, 95% CI 1.07-4.85, p = 0.04) as independent risk factors for glaucoma. The presence of high insertion of iris and IOL implantation in ciliary sulcus may increase the long-term risk of the development of secondary glaucoma after pediatric cataract surgery.