Metal–organic frameworks (MOFs) as a premier class of crystalline porous materials, celebrated for their architectural precision and vast functional versatility in biomedicine. However, the pursuit of crystalline perfection in pristine MOFs often leads to performance bottlenecks in physiological environments, characterized by rigid active sites, restricted mass transport, and suboptimal loading capacities. Defect engineering, the intentional and precise disruption of framework periodicity has recently ascended as a transformative strategy to transcend these intrinsic constraints. By strategically introducing structural imperfections, such as linker vacancies and cluster modulations, MOFs can be endowed with expanded pore volumes, enhanced surface accessibility, and tailored coordination environments that unlock potential enzyme-like activities. Despite the burgeoning interest in Defect-MOFs, a systematic synthesis of the underlying defect-formation mechanisms and their specialized roles in overcoming the limitations of conventional MOFs in biomedical contexts remains elusive. Drawing the rapid evolution of this field, this review provides a timely and critical deconstruction of the synthesis, structure, performance of Defect-MOFs. We systematically categorize advanced synthetic strategies, highlight representative breakthroughs in targeted drug delivery and synergistic theranostics. Finally, we dissect the pressing challenges regarding reproducibility and biocompatibility, offering a strategic roadmap to inspire the rational design of next-generation, Defect-MOFs nanoplatforms for clinical translation.