The objective of this study was to characterize the choroidal morphology and vasculature in pachychoroid diseases (PCD). A total of 49 eyes with polypoidal choroidal vasculopathy (PCV), 43 eyes with neovascular age-related macular degeneration (nAMD), and 50 eyes with central serous chorioretinopathy (CSC), along with 80 healthy eyes, were enrolled in this nested case-control study. The swept-source optical coherent tomography (OCT), OCT angiography, and En face images were quantitatively analyzed. Multivariate logistic regression models showed that older age and increased vessel density (VD) in the choriocapillaris (CC) layer were independent risk factors for both PCV (p(age) < 0.001, p(VD) = 0.004), and nAMD (p(age) < 0.001, p(VD) = 0.005). Decreased VD in the Sattler's layer was an independent risk factor for PCV (p = 0.014). Increased VD in the Haller's layer was an independent risk factor for CSC (p = 0.001). The proportion of the diffuse type of collateral circulation in the Sattler' layer in CSC group was significantly higher than in the other three groups (p < 0.001). We concluded that the involvement of the blood flow in the CC, Haller's, and Sattler's layers are differently affected in CSC, nAMD, and PCV eyes, indicating the different pathological mechanism underlying the phenotype of PCD. The age-dependent establishment of collateral circulation in the Sattler's layer may play a compensatory role regarding ischemic injury in the development of PCD.