Background To compare the choriocapillary flow density (CFD) among the contralateral eyes of polypoidal choroidal vasculopathy (PCV), neovascular age-related macular degeneration (nAMD) and healthy controls with spectral-domain optical coherence angiography tomography (SD-OCTA).Methods This is a cross-sectional study. 36 eyes of 36 PCV patients, 35 eyes of nAMD patients and 34 control eyes were included. All sujects underwent the HD Angio Retina 6.0 mm scan pattern of OCTA (RTVue XR Avanti AngioVue; Optovue, Inc., Fremont, CA, USA). Circles with radius of 1.00, 1.50 and 3.00 mm were manually selected in choriocapillaries (CC) slab, and CFD was calculated as the percentage of flow area to the whole selected area as CFD-1.00, 1.50, 3.00 respectively. Multivariate linear regression analysis was performed to evaluate the differences of CFD among the three groups after adjusting for age, gender and the existence of drusen.Results Mean CFD-1.00, 1.50, 3.00 of nAMD group were 61.09, 62.65 and 65.67, significantly lower than PCV group (65.80, 66.75, 67.86, P= 0.000, 0.000, 0.022) and control (66.17, 66.45, 68.08, P= 0.000, 0.001, 0.025), while no difference were detected between PCV group and control ( P= 0.507, 0.798, 0.575).Conclusions CFD of nAMD fellow eyes were significantly lower than that of PCV and control eyes, while no difference was detected between PCV and control group, indicating different role of CC loss in early pathogenesis of nAMD and PCV.