Fluorescent carbon dots (CDs) represent a promising class of carbon nanomaterials exhibiting excellent optical stability, minimal toxicity, outstanding biocompatibility, and facile surface modification, rendering them ideal for diverse biomedical applications. However, designing CDs with efficient targeting capabilities for precise delivery to disease sites remains a significant challenge. This review provides an overview of recent advancements in the design strategies for targeted CDs, focusing on methods for achieving specific and accurate accumulation in tissues, organs, cells, organelles, and biomolecules. The versatile surface chemistry of CDs, including functional groups and carbon sites, facilitates the development of diverse structures, enabling active targeting through surface modification with targeting ligands, retention of targeting moieties, or utilization of endogenous proteins for targeting purposes. These strategies enhance the specificity and efficacy of CDs for both diagnostic and therapeutic applications, thereby advancing their potential for precise medical interventions. This review provides a comprehensive perspective on elucidating the structure-performance relationship of targeted CDs. Furthermore, the rational construction strategies offer valuable guidance for advancing the development of targeted nanomedicines and their biomedical applications.