Assembly of silica and polymer in the absence of surfactant templates is an emerging strategy to construct intricate nanostructures, whereas the underlying mechanism and structural versatility remain largely unexplored. We report a hierarchical spatial assembly strategy of silica-polymer composites to produce silica and carbon nanoparticles with unprecedented structures. The assembly hierarchy involves a higher length scale asymmetric A-B-A core-shell-type spatial assembly in a composite sphere, and a nanoscale assembly in the middle layer B in which the silica/polymer ratio governs the assembled structures of silica nanodomains. Through an in-depth understanding of the hierarchical spatial assembly mechanism, a series of silica and carbon nanoparticles with intriguing and controllable architectures are obtained that cannot be easily achieved via conventional surfactant-templating approaches. This work opens an avenue toward the designed synthesis of nanoparticles with precisely regulated structures.