This study investigated the toxic effects and mechanisms of trichlorfon (TCF) on the hepatopancreas of Chinese mitten crabs (Eriocheir sinensis). The acute toxicity test results showed that the 96 h-LC50 of TCF on E. sinensis was 4.853 mg/L. We conducted an 8-day short-term exposure experiment with TCF concentrations of 0, 0.061, 0.121, and 0.243 mg/L. The results showed that TCF exposure induces oxidative stress and causes tissue damage and lesions to the hepatopancreas, including hepatic tubules exhibiting disruption, swelling, necrosis, and an ill-defined structure. Transcriptomics revealed differentially expressed genes (DEGs) at the different concentrations, KEGG, and GO enrichment analysis showed that the DEGs were mainly involved in the bile secretion pathway and iron ion binding terms. GSEA was used for single-function enrichment analysis of cell growth and death. We found that DEGs at TCF concentrations of 0.121 and 0.243 mg/L were significantly enriched in the Ferroptosis pathway. Moreover, the synaptic vesicle cycle, GABAergic synapse, and serotonergic synapse were significantly enriched in DEGs at 0.243 mg/L, which indicated that TCF may pose a potential threat to the nervous system. The qPCR detection of Ferroptosis-related genes demonstrated that TCF induces hepatopancreatic Ferroptosis in E. sinensis. We hypothesized that lysosomal autophagy, mainly induced through FTH1 and NCOA4 interactions, released ferric ions, thereby indirectly contributing to Ferroptosis. In addition, WGCNA identified two key modules associated with the phenotype, and further identified the core hub genes were MEX3, RBM46, SLC7A5, and TYR. The results of this study can provide insights into the toxic effects of TCF on aquatic crustaceans.