Apigenin and sodium butyrate have been reported to help alleviate oxidative stress. This study evaluated the jejunal transcriptomic responses in ducks receiving apigenin and sodium butyrate supplementation under oxidative stress. In total, 200 healthy 300-day-old female Jinyun Ma ducks (1.53 kg ± 0.15) were randomly divided into four groups, with five replicates per group. The groups were as follows: a control group (CON): ducks were fed a basal diet with sterile saline injection; a diquat-injection (DIQ) group: ducks were fed a basal diet with diquat injection; an apigenin plus diquat group (API): ducks were fed a basal diet containing apigenin (500 mg/kg) with diquat injection; and a sodium butyrate plus diquat group (SB): ducks were fed a basal diet containing sodium butyrate (500 mg/kg) with diquat injection. The injection dose of diquat is 8 mg/kg body weight. Analysis revealed that the dietary supplementation of apigenin and sodium butyrate reduced malondialdehyde (MDA) levels and increased total antioxidant capacity (T-AOC) (p < 0.05). Compared to the DIQ group, sodium butyrate supplementation during oxidative stress elevated jejunal villus height and villus height/crypt depth ratio in ducks (p < 0.05). The study identified that some candidate genes, including solute carrier family 4 member 3 (SLC4A3), ADAM metallopeptidase domain 12 (ADAM12), and B-cell lymphoma 2-associated-athanogene 3 (BAG3), were significantly upregulated, whereas claudin 23 (CLDN23) and glucose-6-phosphatase catalytic subunit 1 (G6PC1) were markedly downregulated in the API group in comparison with that in the DIQ group (p < 0.05). Collectively, our findings provide molecular evidence for the beneficial effects of apigenin and sodium butyrate against oxidative stress in the jejunum of ducks.