The current study was conducted to investigate the effect of zinc supplementation on the growth performance, intestinal morphology, and the transcription of the barrier function related genes in Pekin ducks. Seven-hundred and sixty-eight 1-day-old Pekin ducks were randomly assigned into six dietary treatments. Each treatment had eight replicates with 16 ducks per replicates. The ducks were fed either a corn-soybean meal basal diet or basal diets supplemented with 15, 30, 60, 120, and 240 mg zinc/kg from zinc sulfate. This experiment lasted for 5 weeks, and the jejunum sample were harvested at 14 and 35 days of age. Results have shown that diets supplemented with zinc significantly increased the duck body weight, average daily gain, and average daily feed intake in different period of experiment (P < 0.05); feed to gain ratio was decreased as the zinc level increased (P < 0.05). Zinc supplementation increased the villus height and decreased the crypt depth in jejunum of ducks (P < 0.05) at 14 and 35 days of age. The transcription of tight junction protein CLDN1, OCND, ZO-1, and ZO-3 in jejunum were increased (P < 0.05), and the messenger RNA (mRNA) levels of leak protein CLDN2 were decreased as the dietary zinc level increased (P < 0.05) at 14 and 35 days of age. The mRNA levels of chemical barrier-related genes MUC2 and TFF-2 in jejunum at 14 and 35 days of age were increased (P < 0.05) by zinc supplementation, and so did the transcription of immunological barrier-related genes lgA, pIgR, LYZ, and AvBD2 (P < 0.05). In conclusion, dietary zinc supplementation exhibited growth-promoting effect on Pekin duck, improved intestinal morphology, and enhanced the intestinal barrier integrity.