This study focused on the medium- and long-chain acylcarnitines (MCACs/LCACs) metabolic axis regulated by peroxisome proliferator-activated receptor alpha (PPARα), aiming to elucidate its potential role in the hepatoprotective effects of herbal medicines. Initially, literature mining and database analysis were conducted to summarize the current research applications of PPARα agonists in liver diseases and the pathological implications of MCACs/LCACs accumulation across different liver disease models. Furthermore, published studies and animal experiments were integrated to validate the potential mechanism by which herbal medicines and herbal ingredients modulate liver disease via the PPARα-MCACs/LCACs pathway. Experimental results showed that co-administration of triptolide and celastrol (TP_Cel) significantly induced liver injury, accompanied by marked accumulation of MCACs/LCACs. In the TP_Cel model, Spearman analysis revealed moderately to strongly inverse correlations between plasma MCACs/LCACs abundances and the expression of hepatic PPARα-target genes, including Cpt1a, Cpt2, and Acox1, with most correlations reaching statistical significance (P < 0.05). In addition, plasma MCACs/LCACs abundances were significantly elevated in Ppara^-/- mice compared with wild-type 129 mice (P < 0.05). Based on these findings, a multi-stage screening strategy was established, resulting in the identification of 68 hepatoprotective herbal medicines (HpHMs) and 29 hepatoprotective herbal ingredients (HpHIs), both targeting PPARα with no documented hepatotoxicity. Finally, molecular docking was employed to preliminarily evaluate the binding capacity of HpHIs to PPARα. These findings provide mechanistic insights and potential resources for the development of herbal medicines and herbal ingredients targeting lipid metabolism disorders in liver diseases. All animal experiments were approved by the Animal Ethics Committee of West China Hospital, Sichuan University (approval No. 20220217001).