Abstract: To study the effects of mitochondrial autophagy and its mechanism in the development of soybean meal-induced enteritis in hybrid yellow catfish(Pelteobagrus fulvidraco♀×Pelteobagrus vachelli♂). A total of 225 hybrid yellow catfish with an initial body weight of (5.11 ± 0.52) g were randomly selected and divided into five treatment groups. β-conglycinin was injected at dose of 0, 0.5, 1.0, 2.0, and 4.0 mg/kg fish body weight into the hindgut of each respective group. After 24 h, hindgut samples were collected for analysis of histopathology, mitochondrial damage, intestinal oxidative stress and inflammation levels, and the expression levels of factors related to the AhR axis, NLRP3, and Hif-1α. β-conglycinin stimulation dose-dependently induced significant histopathological injury, increased intestinal oxidative stress and inflammation levels in the hindgut of hybrid yellow catfish, as evidenced by the shortened mucosal fold length, the widened lamina propria and submucosal layer, inflammatory cell infiltration, and a significant up-regulation of hindgut ROS, MDA levels. The pro-inflammatory factors of il-1β and tgf-α were significantly up-regulated, and the anti-inflammatory factors of il -10 and tgf-β were significantly down-regulated. The microvilli of hindgut epithelial cells were shortened and the intercellular junctional gaps were widen dose-dependently by β-conglycinin stimulation, accompanied by the down-regulated expressions of Zo-1 and Occludin. The intestinal barrier function was does-dependently impaired by β-conglycinin. Further more, the mitochondria in the hindgut epithelial cells exhibit swelling, fragmentation, and vacuolization, with markedly shortened or vanished cristae and severely compromised double-membrane structures. The mRNA expression levels of mitochondrial autophagy-related genes (parkin, pink1, bnip3, fundc1) and autophagy-associated genes (lc3a and lc3b) were significantly upregulated. The results of immunofluorescence showed that the protein expression levels of voltage-dependent anion channel 1 (VDAC1) and the lysosome-associated membrane protein 2 (LAMP2), as well as the intensity of their co-localization, were significantly upregulated. The AhR axis were inhibited and the axis of Hif-1α / NLRP3 were dose-dependently activted by β-conglycinin. β-conglycinin induced enteritis in hybrid yellow catfish in a dose-dependent manner, accompained with the significently damaged mitochondrial structure, the hyperactivated mitophagy of the hindgut epithelial cells, the down-regulated AhR axis and the up-regulated axis of Hif-1α / NLRP3. These fundings suggest that the hyperactivated mitophagy in the hindgut epithelial cells of yellow catfish may serve as the underlying mechanism for soybean meal-induced enteritis. Hif-1α may competitively inhibit AhR expression, ultimately leading to hyperactivation of the mitophagy-NLRP3 pathway and exacerbating hindgut inflammation in hybrid yellow catfish. The findings of this study offer a theoretical basis for identifying molecular regulatory targets to alleviated soybean meal-induced enteritis in hybrid yellow catfish.