Finally, molecular docking, molecular dynamics, drug affinity responsive target stability, and cellular thermal shift assay confirmed that glycitein and isorhapontigenin directly bind to TLR2 to modulate the NF-κB/PPAR-γ signaling, and their anti-NAFLD effects were abolished by TLR2 agonist Pam3CSK4. The gene discussed is TLR2; the disease is metabolic dysfunction-associated steatotic liver disease.