Understanding the fundamental relationships between nanostructural architecture and macroscopic thermal transport behavior is essential for the rational design of next-generation thermal insulation materials. This study presents a systematic investigation of structure–thermal property correlations in hybrid systems composed of MgAl layered double hydroxide (LDH) nanoparticles and silica nanostructures, including mesoporous silica aerogels and hollow silica nanoparticles (HSNs). MgAl-LDH was synthesized via co-precipitation and integrated into silica matrices through in-situ sol–gel processing at varied loadings (0–20 wt%). The resulting hybrids were characterized by X-ray diffraction, Fourier-transform infrared spectroscopy, scanning and transmission electron microscopy, nitrogen adsorption–desorption analysis, and thermogravimetric analysis. Thermal conductivity was correlated with structural parameters including specific surface area (730–1006 m²/g), porosity (93–96%), pore diameter (12–18 nm), LDH loading, and LDH platelet aspect ratio. The Knudsen effect was identified as the primary mechanism underlying the ultra-low gaseous thermal conductivity (λg) within nanoscale pores, while interfacial phonon scattering at LDH–silica boundaries governed solid-phase thermal transport. An optimized 10–15 wt% LDH loading yielded hybrids with thermal conductivity of 25.3–25.9 mW/m·K, enhanced thermal stability (onset decomposition temperature increased by up to 49°C), and reduced calorific value (up to 23.9% reduction), demonstrating that deliberate structural engineering at the nanoscale can simultaneously optimize thermal insulation and fire safety for advanced energy-efficient applications.