Background and aim Previous studies have suggested cardiovascular risk factors increase the risk of not only common sporadic stroke, but also of stroke in patients with monogenic stroke disorders including CADASIL. We investigated the effects of the NOTCH3 Arg544Cys (R544C) variant and associated vascular risk factors on stroke in the Taiwanese population. Methods This study was conducted using data from the Taiwan Biobank, consisting of at least 130,000 Han Chinese participants. The genotype was derived from customized genome-wide arrays for 650,000 to 750,000 single-nucleotide polymorphisms (SNPs). Individuals with NOTCH3 R544C were subsequently matched with noncarriers based on the propensity score at a 1:10 ratio by demographic and cardiovascular risk factors. The odds ratio (OR) for stroke or other phenotypes in NOTCH3 R544C carriers and matched noncarriers was then calculated. Univariate and multivariate regression analyses were performed on cardiovascular risk factors in NOTCH3 R544C carriers with and without stroke. The polygenic risk score (PRS) model, adopted from the UK Biobank, was then applied to evaluate the role of NOTCH3 R544C in stroke. Results From the 114,282 participants with both genotype and questionnaire results, 1,080 (0.95%) harbored the pathogenic NOTCH3 R544C variant. When compared to the matched controls (n=10,800), the carriers presented with a history of stroke (OR: 2.52, 95% CI [1.45, 4.37]), dementia (OR: 30.1, 95% CI [3.13, 289.43]), and sibling history of stroke (OR: 2.48, 95% CI [1.85, 3.34]) phenotypes. The risk of stroke increased with every 10-year increase in age (p = 0.006, Cochran–Mantel–Haenszel test). Among NOTCH3 R544C carriers, 16 (1.3%) of the 1,080 carriers with a stroke history were older, male, and more likely to have hypertension, diabetes, dyslipidemia, and a family history of stroke. In the stepwise multivariate analysis, hypertension (OR: 11.28, 95% CI [3.54, 43.3]) and diabetes mellitus (OR: 4.10, 95% CI [1.31, 12.4]) were independently associated with stroke. Harboring the NOTCH3 R544C variant in the Taiwan biobank is comparable with 6.74 standard deviations increase in individual’s polygenic risk score for stroke. Conclusion While the NOTCH3 R544C variant alone increased the risk of stroke, modifiable vascular risk factors also played a role in the occurrence of stroke in Taiwanese community-dwelling individual carrying NOTCH3 variant.