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Orbital venous malformation results from the aberrant angiogenesis in the orbit; however, the detailed molecular mechanism is still not clear. In this study, tissue samples from 27 patients with orbital venous malformation were collected and subjected to whole exome sequencing. Melanocortin 4 receptor was the gene with highest incidence (7/27) of mutation identified in this series. A total of four types of mutations were found in the coding region and the 5ʹ-untranslated region of melanocortin 4 receptor. All these mutations resulted in the upregulation of melanocortin 4 receptor expression. In vitro assays using human umbilical vein endothelial cells demonstrated that the endothelial properties including cell proliferation, cell cycle, cell migration, and tube formation are positively correlated with the expression level of melanocortin 4 receptor. Melanocortin 4 receptor mutations resulted in increased cAMP production in a cell-based assay. By RNA sequencing technique, melanocortin 4 receptor was found to modulate the downstream genes of PI3K/AKT/mTOR pathway, including p21, cyclin B1, ITGA10, and ITGA11, which are known to regulate the endothelial properties. These data demonstrated that mutations in melanocortin 4 receptor modulate the downstream signaling pathway, facilitate the angiogenic activity of endothelial cells, and therefore is one potential mechanism of orbital venous malformation pathogenesis. Impact statement The detailed molecular mechanism of orbital venous malformation (OVM) is still not clear. Using whole exome sequencing, 4 types of melanocortin 4 receptor (MC4R) mutation were detected in 7 of 27 patients with OVM, and all types of MC4R mutations resulted in the upregulation of MC4R expression. In vitro study indicated that MC4R has impacts on the proliferation, cell cycle, migration, and tube formation of the endothelial cells. Moreover, MC4R mutations altered the downstream signaling, including cAMP concentration and the expression levels of several PI3K/AKT/mTOR downstream genes, including p21, cyclin B1, ITGA10, and ITGA11. MC4R mutations may lead to the pathogenesis of OVM through modulating the downstream signaling to alter the angiogenic activity of endothelial cells.