The multiscale ordering of colloidal nanoparticles (NPs) endows materials with diverse functions and performances. The controllable and predictable assembly of NPs is essential for the new generation of materials science. This study presents a topology-regulated self-assembly approach in an aqueous environment, utilizing polysorbate 20 (Tween-20) and ultrasmall gold nanoparticles (2, 4, and 8 nm AuNPs). The self-assembly process was governed by polyvalent hydrogen bonding interactions between the amphiphilic Tween-20 and tiopronin-capped NPs, with the amphipathic nature of Tween-20 primarily dictating the transformation from 1D to 3D structures. Notably, the NP size influences the assembly process, with the 2 nm particles demonstrating a well-regulated, pH-stable, and reversible assembly capability. Our findings provide a straightforward approach for controlling the assembly of simple nanoparticles and molecules into higher dimensional nano/microstructures, and close the knowledge gap in how NP size affects interactions within the assembly dynamics.