Objective The objective of this study was to evaluate the clinical effects of modified partial pars plana vitrectomy together with phacoemulsification, intraocular lens (IOL) implantation, posterior capsulectomy, and zonulohyaloidectomy for patients with malignant glaucoma after trabeculectomy or cataract surgery. Design Retrospective, cohort study. Participants Thirty consecutive patients (30 eyes) with malignant glaucoma after trabeculectomy surgery or ultrasonic phacoemulsification of cataract between January 2008 and September 2014 were enrolled. Methods A retrospective analysis of 30 eyes with malignant glaucoma after trabeculectomy surgery for angle-closure glaucoma or ultrasonic phacoemulsification of cataract was performed. All patients underwent modified partial pars plana vitrectomy with zonulohyaloidectomy. Phacoemulsification and IOL implantation was performed in 25 patients with no previous cataract surgery. Preoperative and post-operative ocular parameters were recorded in detail. Main outcome measures Clinical features, anterior chamber depth, best-corrected visual acuity, and intraocular pressure (IOP). Results In these 30 patients, 25 had undergone trabeculectomy surgery and 5 had undergone cataract surgery. The mean axial length was 21.3 ± 0.8 mm. After surgery, mean IOP decreased from 34 ± 8.3 mm Hg to 10.5 ± 4.1 mm Hg (Po0.001), and mean anterior chamber depth increased from 0.8 ± 0.4 mm to 2.7 ± 0.3 mm (Po0.001). No severe complications occurred. Conclusions Modified partial pars plana vitrectomy combined with phacoemulsification, IOL implantation, posterior capsulectomy, and zonulohyaloidectomy not only simplifies the process of traditional vitrectomy, but effectively resolves the ciliary block and corrects the misdirection of aqueous humor in malignant glaucoma.