The wall-to-lumen ratio (WLR) of retinal blood vessels promises a sensitive marker for the physiological assessment of eye conditions. However, in vivo measurement of vessel wall thickness and lumen diameter is still technically challenging, hindering the wide application of WLR in research and clinical settings. In this study, we demonstrate the feasibility of using optical coherence tomography (OCT) as one practical method for in vivo quantification of WLR in the retina. Based on three-dimensional vessel tracing, lateral en face and axial B-scan profiles of individual vessels were constructed. By employing adaptive depth segmentation that adjusts to the individual positions of each blood vessel for en face OCT projection, the vessel wall thickness and lumen diameter could be reliably quantified. A comparative study of control and 5xFAD mice confirmed WLR as a sensitive marker of the eye condition.