To investigate the potential of ferulic acid (FA) in attenuating the deleterious effects of oxidized fish oil (OF) on Macrobrachium nipponense, four experimental diets were formulated: 3% fresh fish oil (CT group, peroxide value: 2.2 mmol/kg), 3% oxidized fish oil (OF group, peroxide value: 318 mmol/kg), and 3% OF with an additional 160 and 320 mg/kg of FA (OF+FA160 group and OF+FA320 group, respectively). M. nipponense (initial weight: 0.140 ± 0.015 g) were randomly divided into four groups with six replicates (60 individuals per replicate) and reared for a period of 10 weeks. The results showed that the OF treatments significantly reduced the growth performance, the expression of antioxidant genes in the hepatopancreas, the levels of low-density lipoprotein cholesterol, and the gene expression levels of ACC, FAS, FABP10, ACBP, G6PDH, and SCD in the hepatopancreas (p < 0.05). OF supplementation significantly increased the levels of high-density lipoprotein cholesterol in hemolymph and the gene expression levels of CPT1 (p < 0.05). Addition of FA to the OF group significantly increased total bile acids (p < 0.05). In addition, it was found by Oil Red staining that the proportion of lipid droplets was significantly increased in the OF group (p < 0.05). However, the lipid droplets were alleviated by FA supplementation in the diet. OF was found to significantly reduce the diversity of intestinal microbiota by 16S rDNA sequencing and significantly increase the Firmicutes/Bacteroidetes (F/B) ratio (p < 0.05). Functional analysis of gut microbiota also showed that OF reduced lipolysis and led to fat deposition, which is related to gut microbiota. However, this study found that the composition of the gut microbiome of M. nipponense was changed by the addition of FA in the diet, including an increase in the abundance of Ruminococcaceae UCG-005 and Lachnospiraceae, a reduction in the F/B ratio, and an improvement in lipid metabolism. In conclusion, the OF induced oxidative stress, disturbed the balance of intestinal microbiota, promoted lipid accumulation, and caused disorders of lipid metabolism in M. nipponense by increasing lipid synthesis and reducing β-oxidation. However, the results of this study highlighted the potential of FA supplementation to modulate intestinal microbial composition, promote bile acid production, and activate genes related to lipid metabolism in the hepatopancreas, ultimately leading to a reduction in lipid deposition in M. nipponense.