Venous thromboembolism (VTE), including pulmonary embolism (PE) and deep vein thrombosis (DVT), is considered as one of the most common cardiovascular diseases in the world, causing a huge social and economic burden. Despite the predominant role in the treatment of VTE, anti-thrombotic therapy has an extremely high risk of bleeding due to its association with blood coagulation and hemolysis system. Therefore, strict monitoring should be performed during the disease progression. However, the existing approaches can not fully meet the needs of precision medicine. Molecular imaging can reflect the disease information at the molecular level. Quantitative monitoring on thrombus-targeted nanoprobes through imaging approaches can accurately diagnose disease subtypes and provide personalized treatment. This article reviews the research progress of nanomolecular imaging in the diagnosis and treatment of VTE in recent years, which is expected to provide new ideas for the diagnosis and treatment of VTE.