Herein, we report an example of using scanning transmission electron microscopy to determine the mass-per-length of supramolecular nanofibers. Together with the measurement of the diameter of nanofibers via transmission electron microscopy, we could estimate the packing density of assembling molecules along the nanofibers. A parallel unbiased de novo simulation screens and reveals the most plausible molecular packing pattern of small molecules along the supramolecular nanofibers. Remarkably, the simulated packing patterns and density correlate well with the experimental measurements. Unexpectedly, the naphthalene groups are likely facing outward, creating a hydrophobic surface, which is driven by the geometry of the hydrogelator molecule. Overall, this study establishes a complementary method to determine molecular arrangement along the supramolecular nanofibers, which is potentially useful for the guidance of rational design of biomaterials based on self-assembly.