The study attempted to identify clinical characteristics associated with structural progression in open-angle glaucoma (OAG) in the presence of MvD in different locations. A total of 181 consecutive OAG eyes (follow-up 7.3 ± 4.0 years), which demonstrated peripapillary choroidal MvD (defined as a focal capillary loss with no visible microvascular network in choroidal layer) on optical coherence tomography (OCT) angiography (OCTA), were divided based on the location of MvD. Structural progression was determined using trend-based analysis of the Guided Progression Analysis software of Cirrus OCT. MvD was identified in the temporal quadrant in 110 eyes (temporal MvD; 60.5 ± 12.6 years), and in the inferior quadrant in 71 eyes (inferior MvD; 60.3 ± 11.1 years). After adjusting for age, average intraocular pressure (IOP) and baseline retinal nerve fibre layer (RNFL) thickness and visual field mean deviation, inferior MvD eyes showed faster rates of thinning in the inferior RNFL (mean (95% CI); -0.833 (-1.298 to -0.367)) compared to temporal MvD eyes (-0.144 (-0.496 to 0.207)) when long-term IOP fluctuation was larger than the median value (1.7 mmHg; P = 0.022). Long-term IOP fluctuations were independently associated with inferior RNFL thinning in eyes with inferior MvD (P = 0.002) but not in eyes with temporal MvD. In OAG eyes, the rates of RNFL and GCIPL thinning were comparable regardless of MvD locations. However, inferior MvD is associated with faster RNFL and GCIPL thinning in the same quadrant when long-term IOP fluctuation is present. Structural progression in the presence of temporal MvD was less associated with IOP fluctuation.