ABSTRACT: Triptolide (TP), the major active component in Tripterygium wilfordii Hook. f. (Tripterygium Glycosides), contributes to treat rheumatoid arthritis and anticancer activities. However, the organ toxicity, especially nephrotoxicity and hepatotoxicity limit its clinical application. To fully understand the mechanism underlying the triptolide induced toxicity, iTRAQ based proteomics and targeted fatty acids analysis were performed. In the present study, mouse were treated with LD50 dose of triptolide, and plasma, liver and kidney tissues were harvested before drug administration (0 h) and after drug administration (0.5 h, 1 h, 2 h, 8 h, 16 h). The blood biochemical levels (ALT, AST, BUN and CRE) were used to evaluated the toxicity of triptolide. 2D-LC-MS/MS approach was used to compare different proteins among groups 0h, 1h, 2h and 8 h. Functional annotation of different proteins in liver between different groups reveals that the top 3 pathways influenced by the TP were acute phase response signaling, antigen presentation pathway and FXR/RXR activation, the molecular and cellular functions which was mainly effected were lipid metabolism and small molecule biochemistry. In kidney, the pathway including LPS/IL-1 Mediated Inhibition of RXR Function, EIF2 Signaling, acute phase response signaling, and LXR/RXR Activation were mainly affected. The proteomics data implicated that fatty acids (FAs) may involve in the organ toxicity induced by TP. Then targeted fatty acids analysis was carried out to determinate the concentration between the different groups (0.5 h, 1 h, 2 h, 8 h, 16 h) by HPLC-MRM. We found that fatty acids in liver (C17:0, C18:0, C18:2, C18:3, C20:0, C20:3, C20:4, C22:1, C22:2, C22:3, C22:4, C22:5, C22:6, C24:0, C24:1, C24:2, C24:3, C24:4, C24:5, C24:6) show significant difference among groups, while in kidney, FAs (C12:0, C12:1, C14:0, C14:1, C16:1, C16:2) show significant difference. P450 protein family show significant change in different group, protein CYP4A14 demonstrate change in both kidney and liver tissues. By combing proteomics and targeted FAs analysis, we deeply investigated the mechanism underlying the TP induced organ toxicity, and the results may provide deeply insight into prevention or intervention in the TP clinical usage and improving its safety.