Solids can be generally categorized by their structures into crystalline and amorphous states with different interactions among atoms dictating their properties. Crystalline-amorphous hybrid structures, combining the advantages of both ordered and disordered components, present a promising opportunity to design materials with emergent collective properties. Hybridization of crystalline and amorphous structures at the sublattice level with long-range periodicity has been rarely observed. Here, we report a nested order-disorder framework (NOF) constructed by a crystalline matrix with self-filled amorphous-like innards that is obtained by using pressure to regulate the bonding hierarchy of Cu12Sb4S13. Combined in situ experimental and computational methods demonstrate the formation of disordered Cu sublattice which is embedded in the retained crystalline Cu framework. Such a NOF structure gives a low thermal conductivity (~0.24 W·m−1·K−1) and a metallic electrical conductivity (8 × 10−6 Ω·m), realizing the collaborative improvement of two competing physical properties. These findings demonstrate a category of solid-state materials to link the crystalline and amorphous forms in the sublattice-scale, which will exhibit extraordinary properties.