Didancao (Elephantopus scaber L.) has been used as a traditional herbal medicine and has exhibited a beneficial role in animal health. This study aimed to investigate the effects of dietary supplementation with E. scaber on growth performance, meat quality, intestinal morphology, and microbiota composition in ducks. A total of 480 Jiaji ducks (42 days old, male:female ratio = 1:1) were randomly assigned to one of four treatments. There were six replicates per treatment, with 20 ducks per replicate. The ducks in the control group (Con) were fed a basal diet; the three experimental groups were fed a basal diet supplementation with 30 (T1), 80 (T2), and 130 mg/kg (T3) of E. scaber. After a 48-day period of supplementation, growth performance, meat quality, intestinal morphology, and microbiota composition were evaluated. The results showed that no differences were observed in the final body weight, average daily feed intake, and average daily gain among the four groups. Compared with that in the Con group, the feed conversion in the T1 and T2 groups was increased significantly; the T2 group was shown to decrease the concentration of alanine aminotransferase in serum; the T3 group was lower than the Con group in the concentration of aspartate aminotransferase and was higher than the Con group in the concentration of high-density lipoprotein-cholesterol. The highest concentration of creatinine was observed in the T1 group. The T2 group was higher than the Con group in the contents of Phe, Ala, Gly, Glu, Arg, Lys, Tyr, Leu, Ser, Thr, Asp, and total amino acids in the breast muscle. Moreover, the T2 group was higher than the Con group in the contents of meat C18:2n−6 and polyunsaturated fatty acid. The concentration of inosinic acid in the T1, T2, and T3 groups was significantly higher than that in the Con group. However, the Con group was higher than the T2 or T3 group in the Zn content. The T2 group was lower than the Con group in the jejunal crypt depth. The T3 group was higher than the Con group in the ileal villus height and the ratio of villus height to crypt depth. In addition, the T3 group had a trend to significantly increase the abundance of Fusobacteria. Compared with the Con group, the T1 and T2 groups displayed a higher abundance of Subdoligranulum. Collectively, dietary supplementation with 80 mg/kg of E. scaber improves meat quality and intestinal development in ducks.