Metal‐organic frameworks (MOFs) are lagging in the use of lithium‐ion batteries (LIBs), ascribing to full coordination between metal nodes and organic ligands, to a large extent. By integrating a modulator into a ligand with missing bridging functionality, this study elucidates the role of non‐bridging defect sites in MOFs in tailoring lithium storage performance. A fully bridged pristine MOF (p‐MOF) utilizing the meso‐tetra(4‐carboxylphenyl) porphyrin ligand is compared with a modified MOF containing non‐bridging defects (d‐MOF) introduced by a homologous ligand, tris(4‐carboxyphenyl) porphyrin. Spectroscopic and cryogenic low‐dose electron microscopy techniques verify the presence of non‐bridging defect sites in the d‐MOF and reveal their explicit local structure. Density functional theory calculations show significantly enhanced Li+ adsorption energies and reduced Li+ migration barriers at the non‐bridging sites in the d‐MOF compared to the fully bridging sites in the p‐MOF. As a result, the d‐MOF exhibits exceptional lithium storage performance, achieving a high capacity of 761 mAh g−1 at 0.05 A g−1 and superior rate performance of 203 mAh g−1 at 5 A g−1, which substantially outperform the p‐MOF. This study highlights the potential of modulating MOFs with non‐bridging defects to develop high‐performance LIBs.