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Thrombosis is a leading cause of vascular occlusion in life-threatening cardiovascular emergencies, where current diagnostics are hindered by tenuous spatiotemporal resolution limiting early clot detection, and conventional thrombolytics suffer from poor selectivity causing severe hemorrhagic complications. Advanced nanomaterials offer transformative solutions through tailorable physicochemical properties and a multifunctional design. This review focuses on three key dimensions: (1) targeting strategies, where nanocarriers achieve thrombus-specific accumulation via active ligand–receptor recognition and passive pathological entrapment, (2) diagnostic innovations, where functionalized nanoprobes significantly enhance the sensitivity and specificity of ultrasound, CT, MRI, fluorescence, and photoacoustic imaging, enabling precise localization, compositional analysis, and dynamic monitoring of thrombi, and (3) therapeutic advances, where stimuli-responsive nanosystems achieve spatiotemporally controlled drug release triggered by the thrombotic microenvironment (pH, reactive oxygen species, thrombin, shear forces), and integrated theranostic platforms combine real-time imaging guidance with energy-driven therapies (photothermal, photodynamic, ultrasound) for synergistic thrombolysis. Despite these remarkable advances, there are still formidable bottlenecks in clinical translation, including long-term biosafety, batch-to-batch reproducibility, and the predictive gap of preclinical models. Future progress focuses on interdisciplinary efforts in bioinspired design, multiscale characterization, and the development of dynamic biomimetic testing platforms to accelerate the realization of safe and effective nanotheranostics for precision management of thrombosis.