One of the most extensively applied animal feed additives is yeast culture ( YC ), which can increase production efficiency by altering gastrointestinal tract ( GIT ) microbiota. Geese are the ideal model to study the interaction between diet and GIT, due to their adaptation to consume different roughage sources. Here, we fed geese with 0 (control), 0.5% (treat1), 1.0% (treat2), 2.0% (treat3), and 4.0% (treat4) of YC for 10 wk. The GIT microbiota was analyzed by 16S rRNA gene V3–V4 region via high-throughput sequencing. The results showed that YC supplementation did not significantly affect α-diversity ( P >0.05). However, dietary YC at 2.0% had the highest species richness (quadratic, P < 0.05). Principal coordinates analysis showed an obvious separation between control and 4.0% group. The dominant phyla were Firmicutes and Bacteroidetes whereas the predominant genera were Alistipes and Desulfovibrionaceae . The relative abundance of phyla Firmicutes significantly increased in 0.5, 1.0, and 2.0% group and decreased in 4.0% group ( P < 0.05). YC supplementation increased the relative abundance of Bacteroidetes (linear, P = 0.04) and genus Bacteroides (linear, P = 0.02; quadratic, P = 0.05). 1.0% group contained the highest proportion of the beneficial bacteria, such as Parabacteroides, Enterococcus, Streptococcus , and Pseudomonas . 0.5% group obviously improved the capacity of amino acid and carbohydrate metabolism. Collectively, these findings demonstrate the beneficial effects of YC feeding on gut microbiota for geese, which suggested that dietary strategy based on feed additives is an effective method to maintain the health of geese.