We report the development of an automated method to measure morphological features of the retinal pigment epithelium (RPE), Bruch's membrane (BM) and choriocapillaris (CC) using a commercially available swept source OCT (SS-OCT) system. The locations of the inner segment/outer segment (IS/OS), RPE and CC were determined by optical coherence tomography (OCT) and OCT angiography (OCTA) A-scan intensity profiles, which were used to calculate the mean IS/OS-to-RPE distance, mean RPE-to-CC distance, mean RPE-to-CC outer boundary distance, mean RPE thickness and mean CC thickness across the entire scan volume. The automated method was tested on two groups of normal subjects: younger age group (n=20, 30.3 ± 5.72 years, axial length = 24.2 ± 0.96 mm) and older age group (n=20, 80.8 ± 4.12 years, axial length = 23.5 ± 0.93 mm). The 6×6 mm macular scans were acquired from one eye of each subject. Repeatability of the measurements showed a coefficient of variance < 5% for all the cases. CC locations were confirmed qualitatively with pixel-by-pixel moving of the en face OCT/OCTA images. Relative distance and thickness maps of the RPE-BM-CC complex were generated for visualization of regional changes. We observed thinner CC, thinner RPE and increased RPE-to-CC distance in the older age group. Correlation between CC thickness and choroid thickness suggests that the CC thins with the overall thinning of the choroid. These metrics should be useful to reveal more morphological details of RPE-BM-CC complex, provide a better understanding of the CC in three dimensions, and further investigate potential functional relationships between RPE, BM and CC, and their involvement in age-related ocular diseases.