The understanding of nanomaterials for targeted cancer therapy is of great importance as physical parameters of nanomaterials have been shown to be strong determinants that can promote cellular responses. However, there have been rare platforms that can vastly tune the core of nanoparticles at a molecular level despite various nanomaterials employed in such studies. Here we show targeted photodynamic therapy (PDT) with Zr(IV)-based porphyrinic metal-organic framework (MOF) nanoparticles. Through a bottom-up approach, the size of MOF nanoparticles was precisely tuned in a broad range with a designed functional motif, built upon selection of building blocks of the MOF. In particular, molecular properties of the porphyrinic linker are maintained in the MOF nanoparticles regardless of their sizes. Therefore, size-dependent cellular uptake and ensuing PDT allowed for screening of the optimal size of MOF nanoparticles for PDT while MOF nanoparticle formulation of the photosensitizer showed better PDT efficacy than that of its small molecule. Additionally, Zr6 clusters in the MOF enabled an active targeting modality through postsynthetic modification, giving even more enhanced PDT efficacy. Together with our finding of size controllability covering a broad range in the nano regime, we envision that MOFs can be a promising nanoplatform by adopting advanced small molecule systems into the tunable framework with room for postsynthetic modification.