Our purpose is to evaluate long-term changes in corneal endothelial cells after Ex-PRESS shunt implantation for the treatment of glaucoma in Chinese patients by comparison with the contralateral eye. In this retrospective observational study, glaucoma patients with a single eye undergoing Ex-PRESS shunt implantation surgery were consecutively enrolled. For each patient, the clinical assessment, including corneal endothelial cell density (CECD) before surgery and at 6, 12 months, and at last follow-up (2.43 ± 0.63 years) after surgery was reviewed. The operated eyes were in the study group and the unoperated contralateral eyes were used as the control group to compare the CECD change. A total of 48 subjects (age, 51.02 ± 17.96 years) were included. The follow-up period was 2.08~3.17 years, with an average of 2.43 ± 0.63 years. At the last follow-up after the surgery, the CECD decrease in the operated eyes (5.0%) was similar to that in the contralateral eyes (3.2%) (p = 0.130). There were no significant differences in CECD reduction between the two groups at baseline and each postoperative follow-up (6 months, 12 months and at the last follow-up) (all p > 0.05). The average IOP reduction after the surgery was 50.8%, and the number of IOP-lowering medications was significantly reduced (p < 0.05). In addition, visual acuity showed no significant differences during follow-up (p > 0.05). In this study, we found that the CECD reduction of Ex-PRESS shunt-implanted Chinese eyes was similar to that of contralateral eyes without surgery.