<p>The fold-thrust belt in eastern Sichuan exhibits a unique Jura-type Mountain landscape, characterized by the development of the Middle and Lower Triassic karst aquifers within anticlines (T₂<i>l</i> and T₁<i>j</i> formations, respectively), where both cold and warm springs are present. However, previous studies have focused primarily on warm spring genesis, neglecting a comprehensive understanding from the perspective of groundwater flow system. This study integrates regional tectonic settings, karst hydrogeology and diverse groundwater sample data (karst cold springs, warm springs, boreholes, tunnel drainage, and deep wells). Hydrochemistry, stable isotopes (δ²H, δ¹⁸O), and radiocarbon (¹⁴C) and tritium (³H) age analyses reveal a three-level nested karst groundwater flow system. Enrichment of Mg²⁺ in the groundwater is one effective indicator of a longer residence time in karst aquifers, which can be used to identify and divide the hierarchically flow system. Additionally, age analysis indicates a regional groundwater system over 10,000 years old, an intermediate system spanning a century, and a local flow system comprising modern water. Finally, we proposed a conceptual model of a hierarchically nested karst groundwater flow pattern: regional thermal water primarily originates from high-altitude rainfall, emerging as medium-low temperature warm springs in the gorges or drained by boreholes. Local flow systems, recharged by near source, manifest as karst cold springs in the shallow-cut valleys, with intermediate flow systems developing in between. This study deepens the understanding of the karst groundwater circulation laws in high-steep anticline areas, and enriches the application of the Tóth multi-level nested flow system theory, and provides an important scientific basis for the evaluation, management, and protection of regional groundwater resources.</p>