Two hundred and forty 50-week-old healthy Linwu ducks were randomly assigned to 5 groups with 6 replicates in each group and 8 ducks per replicate. The control group(group 1) was fed with basal diet added 0.2 mg/kg(calculated by selenium) of sodium selenite, group 2, 3, 4, 5 added 0.1, 0.2, 0.3, 0.4 mg/kg(calculated by selenium) of digluconate selenite to the basal diet respectively. The pre-trial period lasted 7 days. The trial period was 63 days. The morphology of duodenum, jejunum and ileum and the microbial diversity of ileum and cecum of the ducks were measured to evaluate the effects. The results showed compared with the control group, the addition of digluconate selenite in the diet had no significant effect on the villus height, crypt depth, intestinal wall thickness, the ratio of villus height to crypt depth of the duodenum, jejunum and ileum. The relative abundance of Proteobacteria and Escherichia-Shigella in the ileum and Proteobacteria and Anaerobiospirillum in cecum of the test group supplemented with digluconate selenite decreased. The relative abundance of Intestinibacter in the ileum and Bacteroidetes, Prevotella_7, Intestinibacter, Rikenellaceae_RC9 in cecum of the test group with the addition of digluconate selenite increased. The number of OTU in the ileum of group 2 was significantly higher than that of the control group. The intestinal microflora α diversity was the highest, which increased the relative abundance of Firmicutes in the ileum and decreased the relative abundance of Escherichia-Shigella. The results of microbial diversity showed that dietary digluconate selenite reduced the relative abundance of harmful microorganisms in the ileum, which was beneficial to intestinal health, and the appropriate addition amount of the dietary digluconate selenite was 0.1 mg/kg(calculated by selenium).