Purpose Functional changes have been observed between diseased and healthy subjects, and functional brain atlases derived from healthy populations may fail to reflect functional characteristic of the diseased brain. Therefore the aim of this study was to generate a visual atlas based on functional connectivity from primary open-angle glaucoma (POAG) patients and to prove the applicability of the visual atlas in functional connectivity and network analysis. Methods Functional magnetic resonance images were acquired from 36 POAG patients and 20 healthy controls. Two data-driven approaches, K-means and Ward clustering algorithms, were adopted for visual cortices parcellation. Dice coefficient and adjusted Rand index were used to assess reproducibility of the two approaches. Homogeneity index, silhouette coefficient, and network properties were adopted to assess functional validity for the data-driven approaches and frequently used brain atlas. Graph theoretical analysis was adopted to investigate altered network patterns in POAG patients based on data-driven visual atlas. Results Parcellation results demonstrated asymmetric patterns between left and right hemispheres in POAG patients compared with healthy controls. In terms of evaluating metrics, K-means performed better than Ward clustering in reproducibility. Data-driven parcellations outperformed frequently used brain atlases in terms of functional homogeneity and network properties. Graph theoretical analysis revealed that atlases generated by data-driven approaches were more conducive in detecting network alterations between POAG patients and healthy controls. Conclusions Our findings suggested that POAG patients experienced functional alterations in the visual cortices. Results also highlighted the necessity of data-driven atlases for functional connectivity and functional network analysis of POAG brain.