An investigation into the possible substitution of Clostridium autoethanogenum protein (CAP) for soybean meal (SBM) in the diet of grass carp (Ctenopharyngodon idellus) was carried out. During a 56-day feeding trial, 750 grass carp were fed five experimental diets with different levels of CAP: SBM (control group), CAP25, CAP50, CAP75, and CAP100, corresponding to dietary SBM replacements levels of 0%, 25%, 50%, 75%, and 100%. The results showed that dietary CAP significantly increased FW, WGR, and PER in CAP25 group (P < 0.05), but complete substitution showed the opposite trend (P < 0.05). The liver antioxidant capacity was improved in CAP25 group manifested by the enhanced SOD, GPx and CAT activities, reduced ROS, and MDA contents, and the up-regulated cuznsod, mnsod, gpx1, gpx4, gsto and gr transcript levels mediated by Keap1-Nrf2 signaling pathway (P < 0.05). The intestinal inflammation was relieved in CAP25 group evidenced by the down-regulated il-β, il-6 and tnf-α expressive abundance through NF-κB pathway (P < 0.05). Additionally, the intestinal mucosal barrier function was enhanced by the upregulation of tight junction proteins (occludin, zo-1 and zo-2) in the CAP25 group. Whereas the intestinal folds showed varying degrees of breakage in CAP100 group. The increased amylase and lipase activities, intestinal folds height, and goblet cell numbers were found in CAP25 group (P < 0.05). The gut microbiota revealed no significant differences in the alpha diversity indices across treatments (P > 0.05). Besides, the abundance of Bacteroides in the CAP25 group was increased, while the abundance of Erysipelatoclosridium in the CAP100 group was increased. Summarily, CAP could replace 25% of SBM with positive influences on growth, antioxidant capacity, immunity and intestinal microbiota for juvenile grass carp. Conversely, high levels of CAP impaired intestinal physical barrier and caused intestinal microbiota disturbance, resulting in negatively affect the growth performance.