Nanomineral opal-CT, a naturally occurring precursor to quartz, is formed through diverse geological processes, including weathering, biological precipitation, hydrothermal alteration, and shock metamorphism. Its formation is integral to the genesis of siliceous rocks and influences abiotic and biogenic interactions within natural systems. Recent discoveries of hydrous opal-CT on the surfaces of Mars and the Moon, identified through microanalysis and remote sensing, have intensified research interest in its structural characteristics. This study investigates the local atomic arrangements in natural opal-CT samples exhibiting varying degrees of crystallinity. We employed a synergistic combination of analytical techniques: synchrotron X-ray diffraction (XRD), total X-ray scattering structure factor S(Q) analysis, transmission electron microscopy (TEM), and pair distribution function (PDF) analysis.Our integrated findings reveal that opal-CT primarily consists of interstratified nanodomains of tridymite and cristobalite, characterized by the presence of twins and stacking faults. The S(Q) analysis aids in deconvoluting the XRD patterns, providing more precise peak profiles and enabling a more accurate determination of the degree of structural ordering. TEM imaging, coupled with selected-area electron diffraction (SAED), directly visualizes the nanodomain architecture and associated planar defects. X-ray PDF analysis proves particularly powerful for unveiling detailed information about local structures, defects, and crystallinity within opal-CT. Notably, an increase in the size of ordered domains, along with the emergence and growth of two distinct peaks at 10.01 Å and 11.16 Å in the G(r) plot, correlates with an increased proportion of cristobalite units and enhanced overall crystallinity. The PDF data further indicate the formation of both four- and eight-membered [SiO₄] tetrahedral rings, resulting from twinning and stacking faults within the intergrown tridymite and cristobalite domain. In conclusion, Synchrotron X-ray Techniques and TEM analysis offers unique quantitative insights into the local structural motifs, effective crystalline domain sizes, and the degree of ordering in opal-CT