VTE is a complex disorder with two main manifestations: DVT and PE. Deficiency of natural anticoagulants plays an important role in the pathogenesis of VTE. Antithrombin (AT) deficiency is one of the most common hereditary thrombophilia in Asia. Subjects with AT deficiency have two mutations in the same allele of the SERPINC1 gene: p.Arg45Gln and p.Ser114Arg (Arg13Gln and Ser82Arg, according to the antithrombin mutation database). DNA sequencing, ELISA (enzyme-linked immuno sorbent assay), plasmid transfection, and homology modeling were performed to study the molecular pathophysiological mechanism of the deficiency. Recombinant expression of these mutations demonstrated a relevant functional effect on the p.Ser114Arg mutation, since it almost abolished the secretion of AT to the conditioned medium and increased intracellular retention, while the p.Arg45Gln mutation had negligible effects. Homology modeling showed that some atoms from Arg114 interfered with the atoms of the β-strand, the abstract power between Arg45 and S2 was larger than that between Gln45 and S2, and the electrostatic energy (-617.281 to -452.079 K) was the primary contributor to this difference. The functional mutation responsible for the deficiency of this potent anticoagulant p.Ser114Arg probably has conformational consequences on the folding of the protein leading to its intracellular accumulation and impaired secretion.