Thrombus causes insufficient blood flow and ischemia damages to brain and heart, leading to life-threatening cardio-cerebrovascular diseases. Development of efficient antithrombotic strategies has long been a high priority, owing to the high morbidity and mortality of thrombotic diseases. With the rapid development of biomedical nanotechnology in diagnosis and treatment of thrombotic disorder, remarkable progresses have been made in antithrombotic nanomedicines in recent years. Herein, we outline the recent advances in this field at the intersection of thrombus theranostics and biomedical nanotechnology. First, thrombus diagnosis techniques based on biomedical nanotechnology are presented. Then, emerging antithrombotic nanotherapeutics are overviewed, including thrombus-targeting strategies, thrombus stimuli-responsive nanosystems and phase transition-driven nanotherapeutics. Furthermore, multifunctional nanosystems for combination theranostics of thrombotic diseases are discussed. Finally, the design considerations, advantages and challenges of these biomedical nanotechnology-driven therapeutics in clinical translation are highlighted.