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Abstract Calcium‐silicate‐hydrates (C–S–H) gel, the main binding phase in cementitious materials, has a complex multiscale texture. Despite decades of intensive research, the relation between C–S–H's chemical composition and mesoscale texture remains experimentally limited to probe and theoretically elusive to comprehend. While the nanogranular texture explains a wide range of experimental observations, understanding the fundamental processes that control particles’ size and shape are still obscure. This paper strives to establish a link between the chemistry of C–S–H nanolayers at the molecular level and formation of C–S–H globules at the mesoscale via the potential‐of‐mean‐force (PMF) coarse‐graining approach. We propose a new thermomechanical load‐cycling scheme that effectively packs polydisperse coarse‐grained nanolayers and creates representative C–S–H gel structures at various packing densities. We find that the C–S–H nanolayers percolate at ~10% packing fraction, significantly below the percolation of ideal hard contact oblate particles and rather close to that of overlapping ellipsoids. The agglomeration of C–S–H nanolayers leads to the formation of globular clusters with the effective thickness of ~5 nm, in striking agreement with small angle neutron and X‐ray scattering measurements as well as nanoscale imaging observations. The study of pore structure and local packing distribution in the course of densification shows a transition from a connected pore network to isolated nanoporosity. Furthermore, the calculated mechanical properties are in excellent agreement with statistical nanoindentation experiments, positioning nanolayered morphology as a finer description of C–S–H globule models. Such high‐resolution description becomes indispensable when investigating phenomena that involve internal building blocks of globules such as shrinkage and creep.