AIMS: Genetics and environmental cues boost the development of human diseases. Methylenetetrahydrofolate reductase (MTHFR) is involved in the metabolism of homocysteine, and a common variant rs1801133 of MTHFR has been reported in human cardiovascular diseases. This study aims to providing a novel strategy for patient stratification with specific genetic and metabolic screening, finally for personalized healthcare for patients with thoracic aortic dissection. METHODS AND RESULTS: We corrected the MTHFR variant to generate an isogenic control iPSC line (Isogenic-iPSC) with CRISPR/Cas9 method, and this isogenic-iPSC shared the same other genetic information with our previously established MTHFR-iPSC line, providing a promising approach for analysis the phenotype and mechanism of rs1801133. During the direct differentiation of endothelial cells from both iPSC lines, rs1801133 variant did not affect the endothelial cell fate determination. Without homocysteine, this variant has little effect on endothelial cell function. While administration of homocysteine, the MTHFR-iPSC derived endothelial cells exhibited disrupted mitophagy, increased cell apoptosis and decreased cell viability. Bulk RNA-seq data indicated LAMP3 is a target of homocysteine, activation of LAMP3 might contribute to homocysteine induced the disruption of mitochondrial structure and cell apoptosis. With chemical compounds screening, kaempferol ameliorated the homocysteine-induced cell toxicity by restoring the mitochondrial structure. The direct relationship between homocysteine metabolism and MTHFR rs1801133 variant was investigated, and the molecular target for homocysteine and translational perspective has also been demonstrated. CONCLUSIONS: Collectively, this study provided the direct evidence of a specific genetic variant in MTHFR and homocysteine metabolism. Investigating the molecular mechanism of homocysteine activated LAMP3 on endothelial cell dysfunction and mitophagy could provide novel insights for targeted disease prevention and improving individual outcomes. TRANSLATIONAL PERSPECTIVE: Thoracic aortic dissection (TAD) is a life-threatening cardiovascular disease with a high mortality, lacking effective medical treatment and early diagnosis. Endothelial cells dysfunction has been considered into the development of TAD. Here, we show that MTHFR variant is responsible for the elevated homocysteine in iPSC-ECs, and disrupted mitochondrial structures by homocysteine significantly impaired endothelial function. Understanding the mechanism and translational medicine of homocysteine-induced endothelial toxicity in human with MTHFR variant could benefit the novel strategy for prevention and vessel protection against metabolism injury. Meanwhile, targeting mitophagy and application of small molecule, such as kaempferol, also provide an insight for endothelial protection.