At 100-nanometer length scale, the mesoscopic structure of calcium silicate hydrate (C-S-H) plays a critical role in determining the macroscopic material properties, such as porosity. In order to explore the mesoscopic structure of C-S-H, we employ two effective techniques, nanoindentation test and molecular dynamics simulation. Grid nanoindentation tests find different porosity of C-S-H in cement paste specimens prepared at varied water-to-cement (w/c) ratios. The w/c-ratio-induced porosity difference can be ascribed to the aspect ratio (diameter-to-thickness ratio) of disk-like C-S-H building blocks. The molecular dynamics simulation, with a mesoscopic C-S-H model, reveals 3 typical packing patterns and relates the packing density to the aspect ratio. Illustrated with disk-like C-S-H building blocks, this study provides a description of C-S-H structures in complement to spherical-particle C-S-H models at the sub-micron scale.