Microthrombus is one of the major causes of the sequelae of Corona Virus Disease 2019 (COVID‐19 and leads to subsequent embolism and necrosis. Due to their small size and irregular movements, the early detection and efficient removal of microthrombi in vivo remain a great challenge. In this work, an interventional method is developed to identify and remove the traveling microthrombi using targeted‐magnetic‐microbubbles (TMMBs) and an interventional magnetic catheter. The thrombus‐targeted drugs are coated on the TMMBs and magnetic nanoparticles are shelled inside, which allow not only targeted adhesion onto the traveling microthrombi, but also the effective capture by the magnetic catheter in the vessel. In the proof‐of‐concept experiments in the rat models, the concentration of microthrombus is reduced by more than 60% in 3 min, without damaging the organs. It is a promising method for treating microthrombus issues.