This study was aimed to investigate whether 1-deoxynojirimycin (DNJ) affects the digestion system of young geese and assess whether mulberry leaf, which contains this substance, has disadvantages that compromise its value as poultry feed. One hundred and twenty-eight 12-day-old male Wanxi white geese were randomly assigned into 4 treatment groups. The control group was fed an ordinary diet without DNJ. The other groups namely L-DNJ, M-DNJ, and H-DNJ had their basic diets supplemented with 0.05 mg/g, 0.1 mg/g, and 0.15 mg/g DNJ, respectively. The geese were fed for 6 wk, and the apparent digestibility test was conducted in the last week. Intestinal parameters, digestive organs, and enzymes were determined. 16S rRNA gene sequencing was conducted for cecal flora composition. The results revealed that DNJ decreased body and liver weight and increased feed conversion ratio in comparison with the control (P < 0.05); however, it did not influence the weight and length of the intestine or the pancreas weight. The utilization of organic matter, metabolizable energy, ether extract, acid detergent fiber, and calcium in feed were reduced in the M-DNJ and L-DNJ groups compared with those in the control (P < 0.05); however, the utilization of crude protein was increased in all DNJ-treated groups (P < 0.01). In the H-DNJ group, the usage of soluble phosphorus was also increased (P < 0.05). High-dose DNJ increased the activity of trypsin in the pancreas but reduced those of amylase (P < 0.05) and lipase (P > 0.05) in the pancreas and duodenum. The intestinal villi were short, even impaired, in DNJ-treated groups. High-throughput sequencing data revealed that DNJ supplement reduced the α-diversity indices of the cecal microbiota. The principal component analysis further suggested a difference in community structure between the DNJ treatment groups and control. High-dose DNJ increased the relative abundance of Bacteroides, Escherichia-Shigella, and Butyricicoccus but reduced that of unclassified Ruminococcaceae compared with the control (P < 0.05). In conclusion, changes in the digestive system caused by DNJ seriously affected the metabolism of nutrients in geese and reduced their growth performance. Attention should be paid to the adverse effects of DNJ when using mulberry leaves as poultry feed.