Angiogenesis and activation of vascular endothelial growth factor (VEGF) signaling are tightly regulated under the condition of hypoxic pulmonary hypertension (HPH); therefore, deciphering the regulatory mechanisms associated with VEGF is important. SET domain-containing 3 (SETD3) and VEGF expression in lung tissue during hypoxia exposure and lentivirus. SETD3 treatments were detected by real-time PCR and Western blot analysis. Remodeling of pulmonary vasculature and hypertrophy of the RV were evaluated. The effects of SETD3 over-expression on the interaction between SETD3 and forkhead box protein M1 (FoxM1) at the VEGF promoter and downstream of the VEGF signal pathway during chronic hypoxia were detected. SETD3 lentiviral vector treatment not only inhibited the increase in VEGF expression but also significantly relieved pulmonary vasculature remodeling and hypertrophy of the RV during HPH. The functional interplay between SETD3 and FoxM1 on chromatin may negatively regulate VEGF expression under HPH through the VEGF receptor-extracellular signal-regulated kinase-hypoxia-induced factor-1 signal pathway. SETD3-mediated transcriptional modification of VEGF may be a potential target to inhibit the development of HPH.