Intestinal microbiota disorders can aggravate pulmonary inflammation during acute lung injury (ALI). As a traditional Chinese herb, Rhubarb can regulated the gut microbiota. Therefore, this study was conducted to test the hypothesis that rhubarb alleviates gut microbiota dysbiosis and inflammation. Feces were collected from patients with ALI to detect the gut microbiota using 16S rDNA sequencing. Subsequently, a mouse model of ALI was established using lipopolysaccharide to investigate changes in the gut microbiota, the peripheral blood was attained for detecting the Th17/Treg cell ratio and the serum level of HDAC6 and HDAC9, and the effect of rhubarb treatment on the gut microbiota and Th17/Treg ratio were also evaluated. The results indicated that both the Firmicutes phylum decreased and the Bacteroidetes phylum increased were identified in patients with ALI, which induced the alternation of histone metabolites. The mice models also showed a similar imbalance in the Firmicutes/Bacteroidetes ratio at phylum of level. Rhubarb treatment alleviated the damaged lung tissue, accelerated Alistipes, Clostridium, and Lactobacillus proliferation at the level of genus, increased the level of HDAC6 in both the mice lung tissue and serum, and markedly reduced the Treg cells and increased the Th17 cells in the spleen tissue. The study suggested that both patients and mouse models with ALI presented gut microbiota dysbiosis, and lead to a Th17/Treg cell imbalance in ALI mouse. Rhubarb promoted Alistipes, Clostridium, and Lactobacillus proliferation, increased the HDAC6 concentration, restored the Th17/Treg cell balance, and protected against ALI.