Acute lung injury (ALI) is characterized by severe inflammation. Vitamin D3 is discussed to reduce inflammation in ALI, but the mechanism is not well understood. This study assesses the effect of different calcitriol administration strategies on inflammation and the lung microbiota composition in ALI. In a mouse model, the alveolus and airway pathology are assessed by immunohistology. mRNA expression is determined by Real-Time Quantitative PCR and protein expressions is detected by Western-blotting. The composition of microbiota is performed by 16s DNA high-throughput sequencing. Short-term vitamin D3 supplementation prevents lipopolysaccharide-induced ALI by preventing pro-inflammatory cytokines including interleukin-1𝜷 (IL-1𝜷), interleukin-6 (IL-6), and tumor necrosis factor 𝜶 (TNF-𝜶). In contrast, long-term treatment over 3 days, 6 days, or 10 days had no such effect. Short-term vitamin D3, but not long-term pretreatment significantly reduces the phosphorylation of signal transducer and activator of transcription 3 and suppressor of cytokine signaling 3, but upregulates the phosphorylation of inhibitor of nuclear factor-𝜿-gene binding. Furthermore, an increased relative abundance of Rodentibacter genus in LPS-challenged mice bronchoalveolar lavage fluid is observed, which is sensitive to short-term vitamin D3 treatment, effectively alleviating the Rodentibacter abundance. Correlation analysis shows that the load of Rodentibacter positively correlated with the IL-1𝜷, IL-6, and TNF-𝜶 gene expression. The data support that a single administration of vitamin D3 may work as an adjuvant therapy for acute lung inflammation.