Selective organic transformations using metal-organic frameworks (MOFs) and MOF-based heterogeneous catalysts have been an intriguing but challenging research topic in both the chemistry and materials communities. Analogous to the reaction specificity achieved in enzyme pockets, MOFs are also powerful platforms for regulating the catalytic selectivity via engineering their catalytic microenvironments, such as metal node alternation, ligand functionalization, pore decoration, topology variation and others. In this review, we provide a comprehensive introduction and discussion about the role of MOFs played in regulating and even boosting the size-, shape-, chemo-, regio- and more appealing stereo-selectivity in organic transformations. We hope that it will be instructive for researchers in this field to rationally design, conveniently prepare and elaborately functionalize MOFs or MOF-based composites for the synthesis of high value-added organic chemicals with significantly improved selectivity.