Supramolecular assemblies with diverse morphologies are crucial in determining their biochemical or physical properties. However, the topological evolution and self‐assembly intermediates as well as the mechanism remain elusive. Herein, a dynamic morphological evolution from solid nanospheres to superhelical nanofibers is revealed via self‐assembly of a minimal l‐tryptophan‐based derivative (LPWM) with various mixed solvent combinations, including the formation of solid nanospheres, the fusion of nanospheres into pearling necklace, the disintegration of necklace into short nanofibers, the distortion of nanofibers into nanotwists, and the entanglement of nanotwists into superhelices. It is found that the breakage of intramolecular H‐bonds and reconstruction of intermolecular H‐bonds, as well as the variation of aromatic interactions and hydrophobic effects, are the key driving forces for topological transformation, especially the dimensional evolution. The nanospheres and nanofibers demonstrate discrepant behaviors towards mouse neural stem cell (NSC) differentiation that compared with negligible impact of nanospheres scaffold, the nanofibers scaffold is favorable for NSC differentiation into neurons. The remarkable dynamic regulation of assembly process, together with the NSC differentiation on twisted nanofibers are making this system an ideal model to interpret complex proteins fibrillation processes and investigate the structure–function relationship.