Background: MiR-126 is likely to be closely associated with the threatening disease deep venous thrombosis (DVT). Aim: This study aims to investigate the influence of aberrantly expressed miR-126 on vascular endothelial cell (VEC) apoptosis during DVTand explore how miR-126 functions in it. Methods: MiR-126 inhibition and overexpression in vivo were respectively performed with antagomir and agomir of miR-126. Using a rat traumatic femoral DVT model, VEC apoptosis and miR-126 expression were detected by TUNEL assay and qRT-PCR before thrombogenesis and at different time phases of thrombogenesis. Protein levels of MMPs, Akt, Bcl-2, Bad, and caspase-9 in vascular tissue were measured by western blotting. In vitro, miR-126 interference, and overexpression were performed on human umbilical vein endothelial cells (HUVECs) using miR-126 inhibitor and mimics. After HUVECs were pretreated with CoCl2, cell apoptosis was analyzed using flow cytometry, and RNA/protein levels of miR-126, PIK3R2, PTEN, and phosphorylated Akts were measured with qRT-PC/western blotting. Results: The apoptosis of VECs was increased by miR-126 inhibition and obviously rescued by miR-126 overexpression. PI3K/Akt signal transduction was suppressed by miR-126 inhibition and evidently enhanced by miR-126 overexpression. Consistent with these findings, the downstream proteins (Bcl-2, Bad, and cleaved caspase-9) in PI3K/Akt pathway and the MMPs were remarkably changed by inhibition or overexpression of miR-126. In vitro experiments also showed that PI3K/Akt signaling was strengthened when miR-126 expression was upregulated or inhibited when miR-126 was knockdown. Conclusion: Overexpressed miR-126 inhibits apoptosis of VECs and DVT through targeting the anti-apoptotic pathway PI3K/Akt via PIK3R2. General significance: These findings may provide a new target for the therapy of DVT.