There has been a considerable interest in developing new types of gels based on a network of fibrous aggregate composed of low molecular weight gelators, also known as supramolecular gels (SMGs). Unlike conventional polymer gels with chemical cross-linking, the network formation in SMGs does not involve any covalent bonds. Thus, the network in SMGs has been often regarded as homogenous or less heterogeneous in comparison with that in chemically cross-linked polymer gels. In this study, we have experimentally verified the existence of the network heterogeneity even in SMGs. The thermal motion of probe particles in SMGs, which were prepared from aqueous dispersions of gelators having a different number of peptide residues, PalGH, PalG(2)H, and PalG(3)H, was tracked. The gels were spatially heterogeneous in terms of the network pore size, as evidenced by the variation in the particle motion depending on the location, at which a particle existed. With varying particle size, it was found that the characteristic length scale of the heterogeneity was in the order of (sub)micrometers and was smaller in the order of the PalG(2)H, PalG(3)H, and PalGH gels.