The structure of opal has long fascinated scientists. It occurs in a number of structural states, ranging from amorphous to exhibiting features of stacking disorder. Opal-CT, where C and T signify cristobalite- and tridymite-like interstratification, represents an important link in the length scales between amorphous and crystalline states. However, details about local atomic (dis)order and arrangements extending to long-range stacking faults in opal polymorphs remain incompletely understood. Here, a multilevel modeling approach is reported that considers stacking states in correlation with the abundance of C and T segments as a high-level structural parameter (i.e. not each atom). Optimization accounting for inter-tetrahedral bond lengths and angles and the regularity of the silicate tetrahedra is included as lower levels of structural parameters. Together, a set of parameters with both coarse-grained and atomistic features for different levels of structural details is refined. Structural disorder at the ∼10–100 Å distance scale is evaluated using experimental pair distribution function and diffraction datasets, comparing peak intensities, widths and asymmetry. This work presents a complete multilevel structural description of natural opal-CT and explains many of the unusual features observed in X-ray powder diffraction patterns. This modeling approach can be adopted generally for analyzing layered materials and their assembly into 3D structures.