In this study, we employed MAP1LC3B and SQSTM1 to evaluate mitophagy, in addition, we found that mitophagy-related PINK1 and PARK2 were decreased in EPC from atherosclerosis mice and mitophagy flux data confirmed mitophagy inhibition, which suggested that mitophagy was the major mechanism instead of macroautophagy. This evidence concerns the gene SQSTM1 and atherosclerosis.