<p>Globally, chronic arsenic exposure causes characteristic skin lesions and multi-organ damage. However, early identification of high-risk individuals remains a critical challenge, and reliable epigenetic markers are urgently needed. This study investigated the association between arsenic (+ 3 oxidation state) methyltransferase (<i>AS3MT</i>) promoter methylation in peripheral blood and arsenic-induced skin lesions in a drinking water-exposed population. The potential of <i>AS3MT</i> methylation as an epigenetic biomarker of arsenic toxicity was further evaluated. A total of 135 participants were enrolled, and <i>AS3MT</i> promoter methylation was measured by MALDI-TOF-MS. <i>AS3MT</i> promoter methylation levels were significantly elevated at six CpG sites and CpG_average in individuals with skin lesions compared to controls. Linear regression models revealed that urinary total arsenic (TAs), along with primary and secondary methylation indices (PMI and SMI), was significantly associated with methylation at specific CpG sites. Restricted cubic spline (RCS) analysis confirmed linear dose–response relationships between arsenic exposure and <i>AS3MT</i> methylation without significant non-linear threshold effects. Binary logistic regression demonstrated that elevated methylation at several CpG sites was significantly associated with increased skin lesion risk. A weighted methylation risk score (wMRS) integrating all sites exhibited excellent discriminatory performance, with an adjusted AUC of 0.874. Skin lesion prevalence increased in a dose-dependent manner across wMRS quartiles, from 29.4% in Q1 to 100% in Q4 (<i>p</i>-trend &lt; 0.001). <i>AS3MT</i> methylation at multiple CpG sites significantly mediated the associations between arsenic exposure and skin lesion risk. These findings indicate that <i>AS3MT</i> promoter hypermethylation may serve as an epigenetic biomarker for early risk identification.</p>