Venous thromboembolism significantly contributes to the global disease burden. Anticoagulant and antiplatelet therapies are currently the treatment strategies. However, challenges remain due to hemorrhagic complications and the inability to resolve established thrombi. There is an urgent need for a new generation of antithrombotic agents. Given the fibrin specificity and rapid thrombus dissolution capacity of recombinant tissue plasminogen activator (TPA) protein, along with the significant advantages of mRNA therapeutics in protein replacement, we aim to develop an antithrombotic strategy through the targeted delivery of TPA mRNA to vascular endothelial cells using synthetic lipid nanoparticles (LNPs). A series of amino ionizable lipids were synthesized to create an LNP library, from which the LNP selectively targeting vascular endothelial cells (vtLNP) was selected by a DNA barcode labeling high-throughput screening method. The antithrombotic efficacy and safety of vtLNP loaded with TPA mRNA (vtLNP@TPA) were evaluated in a deep vein thrombosis (DVT) mouse model and normal ICR mice, respectively. The results revealed that vtLNP@TPA significantly prevented the occurrence and development of venous thrombosis. This study provides relevant experimental evidence for a novel antithrombotic therapy strategy for venous thrombosis using mRNA therapeutics.