Purposes: Intestinal microbiota disorders can aggravate pulmonary inflammation during acute lung injury (ALI). Rhubarb, a Chinese herb, can regulated the gut microbiota. Therefore, this study was conducted to test the hypothesis that rhubarb alleviates gut microbiota dysbiosis and inflammation. Methods: 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 periperal blood was attained for detecting the Th17/Treg cell ratio, and the effect of rhubarb treatment on the gut microbiota and Th17/Treg ratio were also evaluated. Results: Rhubarb treatment significantly reduced the Firmicutes abundance and markedly increased the Bacteroidetes abundance in ALI patients. The rat models also showed a similar imbalance in the Firmicutes/Bacteroidetes ratio. Rhubarb treatment alleviated the damaged lung tissue, accelerated Firmicutes proliferation, increased the HDAC6 in both the mice lung tissue and serum, and markedly reduced the Treg cells and increased the Th17 cells in the spleen tissue. Conclusion: We determined that both patients with ALI and mouse models of ALI presented gut microbiota dysbiosis and Th17/Treg cell imbalances. Rhubarb promoted Firmicutes proliferation, increased the HDAC6 concentration, restored the Th17/Treg cell balance, and protected against ALI.