The regulation of natural helical nanostructures is principally supported and actuated by hydrogen bonds (H-bonds) formed from hydrogen-bonding groups (peptide bonds and base pairs) to realize biological activities and specific biofunctional transformations. However, studying the role of H-bonding patterns on the handedness of supramolecular assemblies is still challenging, since supramolecular assemblies will be disassembled or destabilized with slightly varying H-bonding groups for most supramolecules. To circumvent this issue, herein, two types of self-assembled C₂-symmetric phenylalanine derivatives differed by a single H-bonding group (ester or amide) are systematically designed for deciphering the role of H-bonding pattern on the chirality of supramolecular assemblies and their related biostability. Opposite handedness nanofibrous structures with tailorable diameter and helical pitch are achieved with the transition from ester to amide groups in the gelators. Experimental and theoretical evidence suggests that helical orientation of ester-containing gelators ascribes to intermolecular H-bonds. In contrast, the helical direction for the amide-counterparts is mainly due to intra- and intermolecular H-bonds. Moreover, these H-bonding groups greatly influence their stability, as revealed by in vitro and in vivo degradation experiments and the left-handed assemblies are more stable than the right-handed ones. Thus, the study offers a feasible model to have valuable insight into understanding the role of H-bonding patterns in biological folding.