A series of naphthalimide derivative gelators (G-o, G-m, and G-p) with three molecular isomers as their terminal groups were designed and synthesized. Only G-m and G-p could form stable organogels in some solvents including methanol, acetonitrile, n-hexane, toluene, ethanol, DMSO, DMF, and mixed solvents of acetonitrile/H2O (1/1, v/v). The different self-assembly structures were obtained from the self-assembly process of G-o, G-m, and G-p such as structures like a Chinese chestnut formed by irregular micrometer pieces, microbelts, and microbelt structures mingled with the bird's nest structures which exhibited different surface hydrophobicity with water contact angles of 121-139 degrees due to their different intermolecular noncovalent interactions. To our surprise, G-p acetonitrile solution emitted 492 nm light with a red-shift of 72 nm compared with that emitted from G-o and G-m acetonitrile solution under 350 nm light excitation. Three gelators showed different detection abilities toward metal ions. G-o did not have any ability for sensitive and selective detection toward any ion. In contrast, G-m and G-p could sensitively and selectively detect Hg-2(+) and Fe-3(+). The detection limits for Fe3+ and Hg2+ by G-m were 4.76 x 10(-5) M and 7.01 x 10(-6) M with the corresponding association constants (K) of 1.64 x 10(4) and 3.79 x 10(4) M-1, respectively. The detection limits for Fe-3(+) and Hg2+ by G-p were 3.26 x 10(-5) and 1.77 x 10(-6) M with the corresponding K of 1.44 x 10(5) and 1.99 x 10(4) M-1, respectively. More interestingly, the back-titration of SCN-could distinguish Hg2+ from Fe3+. At the same time, xerogels G-m and G-p also exhibited responsiveness toward Fe3+ and Hg2+ through fluorescence changes. The photophysical properties, gel formation, hierarchical structures, surface wettability, and their function in this self-assembly system could be tuned through the molecular isomer effect. This work provides a new research paradigm for molecular isomer tuned supramolecular self-assembly materials from noncovalent interaction to molecular function.