Computational and experimental methods were applied to investigate the self-assembly and gelation of C-13-dipeptides. A modified aggregation propensity (AP(s)) was introduced to correlate the effects of side chains of amino acids on the tendency to aggregate. From the experimental results, the ranges of 0.156 < AP(s) < 0.250 seemed to be a proper region for the C-13-dipeptides to form hydrogels, while other molecules with higher or lower APs were insoluble or dissociated. As observed from molecular dynamics simulations, the C-13-dipeptides first formed small aggregates through hydrophobic interactions and then rearranged through electrostatic attractions and hydrogen bonds for self-assembly. The C-13-dipeptides tended to be antiparallel packed, as shown by hydrogen bonding analyses. Experimental observations and analyses on the structures of C-13-dipeptide hydrogels matched the computational conclusions very well. From the five selected gelators, i.e., C-13-GW, C-13-VY, and C-13-WT, strong pi-pi stacking was observed. For C-13-WS, strong hydrogen bonding was found, and in C-13-WY, both strong pi-pi interactions and hydrogen bonds were found. It takes around 90 min or longer for C-13-dipeptides to form hydrogels, and those formed by C-13-WY and C-13-WS had weak water holding capacities, which might be due to strong intermolecular hydrogen bonding. From rheological studies, the C-13-dipeptides formed strong chemical gels that were stabilized by strong interactions between the molecular aggregates. These gelators exhibit the potentials to be environmentally friendly substitutes for the common functionalized peptide gelators