The connection between electronic structures of metal-organic frameworks (MOFs) and their building subunits is a key cornerstone for rational MOF material design. Some two-dimensional conjugated MOFs were reported to be topological insulators. However, many of them are not intrinsic as the Fermi levels are far from the topological gaps. The subunit-to-MOF electronic orbital correspondence should be established to bridge their chemical structure and physical properties, thus understanding the design rules toward intrinsic topological insulators. Herein we reveal the fundamental role of the subunit-to-MOF symmetry relation in determining their orbital interaction and hybridization and, consequently, topological characteristics. In particular, such honeycomb-kagome MOFs possess delocalized symmetry-enforced nonbonding electronic states with the topological spin-orbit gap. The nonbonding nature of these states allows tailored band structure modulation through molecular structure and strain engineering, with the potential realization of an intrinsic metal-organic topological insulator.