To quantify the effect of long-term high-altitude (HA) exposure on retinal and choroidal microcirculation and to relate these changes to high-altitude polycythemia (HAPC), as a proxy for etiopathogenesis of high-altitude related retinopathy (HAR). Fifty-one HAPC patients, 50 healthy HA residents, and 43 low altitude (LA) residents were recruited in this study. Optical coherence tomography angiography (OCTA) and enhanced depth imaging (EDI)-OCT images were analyzed. Retinal microvascular metrics included vessel density (VD), skeleton density (SD), fractal dimension (FD), and foveal avascular zone (FAZ). Choroidal microvascular metrics included subfoveal choroidal thickness (SFCT) and choroidal vascularity index (CVI). All metrics were calculated by ImageJ software and compared among HAPC group, healthy HA group, and LA group. In HAPC group, VD (30.62 ± 3.67%), SD (13.25 ± 1.64%), FD (1.79 ± 0.04), and the CVI (63.01 ± 1.42%) were significant lower and SFCT (403.25 ± 94.3μm) was significant thicker than healthy HA group (all P < 0.001). FAZ area was comparable between two groups (0.42 ± 0.1 vs. 0.4 ± 0.11 mm2, P = 0.411). However, these metrics were not different between healthy HA group and LA group (all P > 0.05) except for FD was lower in HA group (P < 0.001). Pearson's correlation analyses revealed HGB was negatively related with VD (r = - 0.562, P < 0.001) and positively related with SFCT (r = 0.505, P < 0.001) in healthy HA group; however, no associations between HGB and vascular metrics in HAPC group were detected (all P > 0.05). Long-term exposure to HA environment induces retinal and choroidal microcirculation disturbance in HAPC patients. However, these changes were not evident in healthy HA residents because of adaptation.