Background To compare the efficacy of Ex-PRESS implantation versus trabeculectomy combined with phacoemulsification. Methods A retrospective 12-month study on patients with coincident primary open-angle glaucoma (POAG) and cataract. The patients underwent combined phacoemulsification and Ex-PRESS implant (Phaco-ExPRESS, n = 35) or phacotrabeculectomy (Phaco-Trab, n = 35). The morphological structures of the filtering bleb were examined by slit-lamp, anterior segment optical coherence tomography (AS-OCT) and in vivo confocal microscopy (IVCM). Complete success was defined as postoperative intraocular pressure (IOP) Results No significant difference in the variables such as age, IOP and perimetry was found between the groups of Phaco-ExPRESS and Phaco-Trab. At the one-year postoperative visit for filtering blebs, Phaco-ExPRESS increased the mean area of epithelial microcysts significantly from 0.10 ± 0.05 to 0.20 ± 0.09 μm2 per μm2, while Phaco-Trab decreased the mean area significantly from 0.08 ± 0.04 to 0.04 ± 0.06 μm2 per μm2. Notably, the hyperreflective dots detected by IVCM decreased by 84.9% in Phaco-ExPRESS but increased by 36.3% in Phaco-Trab. The hyperreflective dots were further identified as neutrophil- and monocyte-like cells. The number of these cells were negatively correlated with the microcysts area (r = − 0.7, P P vs. 41.2%, P P P = 0.24). Conclusions At the one-year follow-up, Phaco-ExPRESS generated better filtering bleb with larger area of microcysts, looser connective tissues, and less inflammation than that of Phaco-Trab, providing adequate IOP control and less IOP-lowering medications. These findings indicate that Phaco-ExPRESS could be more preferred than Phaco-Trab for the treatment of patients with coincident POAG and cataract.