C-S-H is a nano sized material with some degree of crystallinity as observed by X-ray diffraction techniques. The underlying atomic structure of C-S-H is similar to the naturally occurring mineral tobermorite. It has a layered geometry with calcium silicate sheet structure separated by an interlayer space. The silicates in C-S-H exist as dimers, pentamers and 3n-1 chain units  (where n is an integer greater than 0) and calcium ions are found to connect these chains making the three dimensional nano structure as observed by dynamic nuclear polarisation surface-enhanced nuclear magnetic resonance.  The exact nature of the interlayer remains unknown. One of the greatest difficulties in characterising C-S-H is due to its variable stoichiometry.
The scanning electron microscope micrographs of C-S-H does not show any specific crystalline form. They usually manifest as foils or needle/oriented foils.
Synthetic C-S-H can be divided in two categories separated at the Ca/Si ratio of about 1.1. There are several indications that the chemical, physical and mechanical characteristics of C-S-H varies noticeably between these two categories.