The present study was carried out to determine whether low dose of zinc oxide nanoparticles (Nano-ZnO) could serve as a potential substitute of pharmacological dose of traditional ZnO in weaned piglets. 180 crossbred weaning piglets were randomly assigned to 3 treatments. Experimental animals were fed basal diet supplemented with 0 mg Zn/kg (Control), 600 mg Zn/kg (Nano-ZnO) and 2000 mg Zn/kg (ZnO) for 14 days. On day 14 after weaning, the piglets fed Nano-ZnO did not differ from those fed traditional ZnO in growth performance and jejunal morphology, while Nano-ZnO treatment could significantly alleviate the incidence of diarrhea (P < 0.05). In jejunum, the mRNA expressions of intestinal antioxidant enzymes and tight junction proteins were increased (P < 0.05) in Nano-ZnO treatment. In ileum, the expression levels of IFN-γ, IL-1β, TNF-α and NF-κB were decreased (P < 0.05). Gene sequencing analysis of 16S rRNA revealed that dietary Nano-ZnO increased the bacterial richness and diversity in ileum, while decreased both of them in cecum and colon. Specifically, the relative abundances of Streptococcus in ileum, Lactobacillus in colon were increased, while the relative abundances of Lactobacillus in ileum, Oscillospira and Prevotella in colon were decreased (P < 0.05). In conclusion, our data reveal that low dose of Nano-ZnO (600 mg Zn/kg) can effectively reduce piglet diarrhea incidence, similar to high dose of traditional ZnO (2000 mg Zn/kg), which may be mediated by improving intestinal microbiota and inflammation response in piglets, and help to reduce zinc environmental pollution.