To investigate the anti-atherosclerosis effect and mechanism of 5-heptadecylresorcinol (AR-C17), a bioactive substance in whole grain foods, human umbilical vein endothelial cells (HUVEC) were induced with trimethylamine-N-oxide (TMAO) to establish adamage model. The protective effect of AR-C17 on HUVEC and its mechanism were investigated by detecting endothlial cell migration, mitochondrial function, apoptosis level and related protein expression. The results showed that 0.5,1.0 and 2.0μmol/L AR-C17 could significantly inhibit TMAO-induced cell death, and the cell viability of HUVEC were increased to 69%, 71% and 72%, respectively. Three dosages of AR-C17 also significantly improved the endothelial function of HUVEC, and the cell migration rates were increased to 47%, 55% and 71%. The result of mitochondrial function showed that AR-C17 could significantly reduce the level of intracellular and mitochondrial reactive oxygen species induced by TMAO and the disorder of mitochondrial membrane potential. AR-C17 significantly increased the basal respiration, ATP production and maximum respiratory oxygen consumption rates, indicating that AR-C17 significantly alleviated the TMAO-induced mitochondrial dysfunction. Meanwhile, the results showed that AR-C17 reduced the TMAO-induced apoptosis rate of HUVEC from 32% to 19%. The expression levels of proteins related to the mitochondria-dependent apoptotic pathway indicated that AR-C17 significantly reduced the ratio of B-cell lymphoma-2 (BCL-2)-associated X protein and BCL-2 expression, while inhibiting cytochrome C expression in the cytoplasm and increasing its expression level in mitochondria. The results showed that AR-C17 alleviated TMAO-induced HUVEC injury by improving mitochondrial function and inhibiting mitochondria-dependent apoptosis. The aim of this study was to provide the theoretical basis for development and utilization of whole grain functional foods against cardiovascular .