The prevalence and residue levels of mycotoxins in food have emerged as a global public health concern, exacerbated by climate change. Despite routine monitoring of mycotoxin residues in foodstuffs by health agencies, comprehensive exposure assessments remain limited due to insufficient food consumption data and complex food classification systems. This study employed the Stochastic Human Exposure and Dose Simulation High-Throughput (SHEDS-HT) model, adapted for the Taiwanese population with National Food Consumption Database (NFCD), to estimate aggregate dietary exposure to six major mycotoxins: aflatoxin B1, ochratoxin A, zearalenone, fumonisin B1, deoxynivalenol, and citrinin. Using Margin of Exposure (MoE) analysis, citrinin was identified as the non-carcinogenic priority mycotoxin, with infants and children being the most vulnerable group due to their higher intake of rice-based products per unit body weight. Additionally, 2.5% and 2.4% of the population exceeded the (provisional) tolerable daily intake (pTDI) for ochratoxin A and aflatoxin B1, respectively, with notable detection in candy, spices, sugar, and peanut-based products. For cancer risk characterization, aflatoxin B1 and ochratoxin A demonstrated MoE values below the critical safety threshold (10,000), indicating potential health risks. This study highlights the urgent need for coordinated surveillance and emphasizes the importance of biomonitoring approaches to better characterize total mycotoxin exposure in Taiwan, providing valuable insights for evidence-based risk management and regulatory strategies.