Accurate identification of acid-producing layers is key to controlling acid mine drainage (AMD) in abandoned coal mines. This study collected 337 core samples from 34 boreholes in the Modigou mining area, Shanxi, China, and established a combined static–mineralogical–kinetic approach to evaluate the acid-generating and neutralization potentials of sulfur-bearing rocks. Three-stage net acid generation (NAG) tests identified the pyrite-bearing layer of the Benxi Formation and the No. 10 coal seam of the Taiyuan Formation as the main acid producers, with NAG values of 360.41 and 97.87 kg H₂SO₄/t, respectively, while the Taiyuan limestone showed a high neutralization capacity (ANC = 490 kg H₂SO₄/t). NAG pH was strongly negatively correlated with sulfur content (Pearson r = −0.75, p < 0.01). Sulfide oxidation acid production showed staged attenuation, with average decreases of 64.81% and 47.65% in the second and third stages. Humidity cell experiments demonstrated continuous acid production over 63 days under dry–wet cycles, with increased acid generation rates at higher flow velocities (Darcy flux: 3.54 × 10⁻³ cm/s for accelerated vs. 8.84 × 10⁻⁴ cm/s for standard conditions). Multi-dimensional flow-through simulations confirmed the AMD formation mechanism of “acid supply, buffer, and fracture conduction”. The identified acid-producing layers matched well with field discharge points. This multi-method coupling system provides a theoretical basis for source control of AMD in abandoned high-sulfur coal mines in the Yellow River Basin. This study did not account for microbial catalysis, which is a key limitation of the static chemical oxidation method used.