Controllable synthesis of hierarchical zeolites from natural aluminosilicate minerals is considered an efficient and eco-friendly approach for the production of high-performance zeolites, but its synthesis mechanism is still obscure. Herein, we take the synthesis of a single-crystalline hierarchical NaA zeolite using submolten salt depolymerized kaolin (SMS-K) as the sole source of silicon and aluminum via a mesoscale reorganization strategy as an example to elucidate the reorganization process. Comprehensive morphological and structural analyses reveal that sodium-rich voids in SMS-K facilitate concurrent assembly both within the interior and at the interface of the amorphous gel, leading to the formation of numerous nanoparticles with short-range order which assemble into single-crystal nanocube NaA zeolites with intracrystalline mesopores. By harnessing confinement effects, SMS-K modulates the growth of nanoparticle sizes and enhances the intimate interconnection of nanocubes, thereby yielding NaA zeolite aggregates that exhibit hierarchical porosity, encompassing micro-, meso-, and macropores. This study offers the potential for designing and precisely controlling the fabrication of hierarchical zeolites derived from natural minerals.