Calcium silicate hydrate (C‐S‐H), the main binder of Portland cement, is one of the most complex nanostructured materials, making the retrieval of its highly defective atomic arrangement a long‐standing challenge. This drawback prevents the development of realistic molecular models to guide the optimization of the physicochemical properties of Portland cement materials. Here, we applied Debye function analysis (DFA), an ab initio X‐ray diffraction (XRD) analysis method suitable to disordered nanostructured materials, to identify the atomic and nanoscale structural‐disorder features that dictate C‐S‐H's scattering properties. By examining the DFA theoretical calculations of C‐S‐H with different sizes, crystal defects, and stacking faults, we discovered that random layer rotations are a critical feature in the C‐S‐H phases, which has been largely overlooked by other XRD analysis methods. Moreover, the DFA calculations disclosed that C‐S‐H consists of layered, plate‐like nanoparticles with ∼10 nm in lateral size and defined crystal defects, in agreement with previous neutron scattering and spectroscopic studies. These findings may not only enable the construction of more accurate nanoscale models of hydrated cement but have potential wider application to similar complex layered structures, such as phyllosilicates, in ceramic and geological materials.