This study aimed to find out the significance of the difference between frequency-doubling technology perimetry (FDT) and standard automated perimetry (SAP) in terms of the detected visual field (VF) damage, and evaluate associated factors to SAP–FDT difference in early glaucoma. Glaucoma patients in early stage (MD better than − 6.0 decibel, 96 eyes) were included in this cross-sectional study. We subtracted mean deviation (MD) and pattern standard deviation (PSD) of FDT from those of SAP, respectively. Additionally, we counted significantly depressed points of P < 5% and P < 1% on the pattern deviation probability plot of both FDT and SAP and defined eyes with significant SAP–FDT difference when the number of abnormal points were greater than 4 points on FDT. We measured lamina cribrosa depth (LCD) and lamina cribrosa curvature index (LCCI) for structural parameters of the optic nerve head from images using enhanced depth imaging of the optical coherence tomography (OCT). Peripapillary vessel density (VD) and presence of microvasculature dropout (MvD), the complete loss of choriocapillaris in localized regions of parapapillary atrophy, was evaluated using deep layer map of OCT angiography (OCT-A) for vascular parameters. Peripheral nasal step (PNS) group had an isolated glaucomatous VF defect within nasal periphery outside 10° of fixation. Parafoveal scotoma (PFS) group had an isolated glaucomatous VF defect within 12 points of a central 10˚ radius. Eyes with significant SAP–FDT difference showed higher detection of MvD on deep layer map of OCT-A, greater LCD, and greater LCCI (all P < 0.05, respectively). In logistic regression analysis, frequent presence of MvD, less presence of disc hemorrhage, and greater LCD were significantly associated with significant SAP–FDT difference. Sub-analysis was performed in eyes with PNS (50 eyes) and PFS (46 eyes). SAP–FDT difference of MD value showed positive association with peripapillary VD on deep layer of OCT-A, which was significant in eyes with PFS compared to eyes with PNS. SAP–FDT difference of PSD value showed negative association with LCCI and LCD, which was significant in eyes with PNS compared to eyes with PFS. Glaucomatous eyes classified by the difference of the detected VF damage on FDT versus SAP showed different clinical features. Greater SAP–FDT difference was significantly associated with structural parameters such as LCD and LCCI. Less SAP–FDT difference was associated with presence of disc hemorrhage and lower deep layer peripepillary VD. There is possibility to use the difference of SAP and FDT to identify associated risk factors in glaucoma patients.