In the rapidly evolving fields of materials science, catalysis, electronics, drug delivery, and environmental remediation, the development of effective substrates for molecular deposition has become increasingly crucial. Ordered mesoporous silica materials have garnered significant attention due to their unique structural properties and exceptional potential as substrates for molecular immobilization across these diverse applications. This study compares three mesoporous silica powders: MCM-41, SBA-15, and SBA-16. A multi-technique characterization approach was employed, utilizing low- and wide-angle X-ray diffraction (XRD), nitrogen physisorption, and transmission electron microscopy (TEM) to elucidate the structure–property relationships of these materials. XRD analysis confirmed the amorphous nature of silica frameworks and revealed distinct pore symmetries: a two-dimensional hexagonal (P6mm) structure for MCM-41 and SBA-15, and three-dimensional cubic (Im$\overline{3}$m) structure for SBA-16. Nitrogen sorption measurements demonstrated significant variations in textural properties, with MCM-41 exhibiting uniform cylindrical mesopores and the highest surface area, SBA-15 displaying hierarchical meso- and microporosity confirmed by NLDFT analysis, and SBA-16 showing a complex 3D interconnected cage-like structure with broad pore size distribution. TEM imaging provided direct visualization of particle morphology and internal pore architecture, enabling estimation of lattice parameters and identification of structural gradients within individual particles. The integration of these complementary techniques proved essential for comprehensive material characterization, particularly for MCM-41, where its small particle size (45–75 nm) contributed to apparent structural inconsistencies between XRD and sorption data. This integrated analytical approach provides valuable insights into the fundamental structure–property relationships governing ordered mesoporous silica materials and demonstrates the necessity of combined characterization strategies for accurate structural determination.