To optimize the utilization of fermented maize stover (FMS) feed during the fattening phase of Xianghai flying geese (XFG), a total of 300 XFG at 125 days of age were randomly assigned to four dietary treatment groups with three replicates of 25 in each set. Group A was fed the basal fattening diet, while the B, C, and D groups were fed the basic fattening diet and diets supplemented with 5%, 10% or 15% FMS, respectively. The findings indicate that the production performance indicators (especially the dressed, eviscerated and breast muscle yield) of Group D closely resembled Group A more than Groups B and C. Intestinal morphometry found that the jejunal villus height and the villus height/crypt depth were significantly increased in Group D compared to Group A. Next, 16S rRNA amplicon sequencing of the extracted DNA revealed that beneficial microbiota (Coprococcus and Victivallis) showed increased abundance in Group D. Cecal flora function analysis further revealed that some amino acid and glycerol biosynthesis were found to be associated with growth performance in geese. These findings suggest that incorporating 15% FMS as a substitute for a portion of the feed during the fattening phase of XFG can effectively sustain their production performance, optimize the gut microbial community and morphometrical traits, provide new insight into using non-conventional feed resources to reduce feed cost and improve economic benefits in the breeding industry.