Metal-organic frameworks (MOFs) have been considered an emerging material for various applications. The fine tunability of both their inorganic nodes and organic ligands make MOFs a good platform for target-specific utilization. Generally, two coordinating groups (e.g., carboxylate) are necessary for MOF formations in case of representative, benzene-dicarboxylic acid type MOFs, and the additional functional groups could be installed in the remaining sites of organic ligands. Various functional groups could be introduced on the ligands such as amino-, halo-, hydroxy-, ether, thiol, and etc. In addition, multiple functional groups could be installed at specific position on the ligand by implementing positional regioisomerism, which helps elucidate the individual effects that each substituent imposes on the organic linkers. Therefore, deliberate structural and functional features can be introduced into a pristine framework. Indeed, this relatively ease functionalizations and positional isomerism of functional groups are the unique features of MOFs compare to other porous materials. In this review, we systematically categorized and described positional regioisomerism with multiple functional groups in MOF organic linkers. Specifically, regioisomeric MOFs bearing two identical groups, two different groups, more than three dissimilar groups, or miscellaneous moieties were discussed in terms of their structures and functions. A comprehensive overview of studies investigating the structures and properties triggered by the different positioning of functional groups in MOF frameworks could provide a base for the molecular design of desirable materials with advanced functionality.