© 2020 The Japan Society for Aeronautical and Space Sciences. Estimating the regolith properties of Phobos' surface is of critical importance for the landing and performance of the Martian Moons eXploration (MMX) sample return mission. Regolith physical properties such as strength, regolith thickness, and the presence of regolith layers are related to morphologies of superposing impact craters. However, the accurate depths of Phobos' sub-kilometer-diameter craters including irregularly shaped craters have not yet been fully characterized. Here, by using our high-resolution (20m/pixel) digital elevation model of the nearside (or the sub-Mars side) of Phobos, we investigate the topographic profiles of the sub-kilometer craters. We confirm the presence of crater rims, and bowl-shaped, central-mound, and flat-floored crater geometries. The topography of one flat-floored crater is consistent with a boundary of regolith layers at a depth of ∼ 160-180 meters. Morphometric measurements of 35 sub-kilometer craters show that their depth-to-diameter (d/D) ratios are in the range of 0.037 and 0.174 (mean value = 0.089, median value = 0.093). This suggests either a surface layer composed of rocky debris that effectively dissipates impact energy and causes a reduction in crater depth, or subsequent resurfacing events changed the original crater topography.