Lactobacillus plantarum can relieve diarrhea caused by enterotoxigenic Escherichia coli (ETEC), but the remission mechanism has not been fully explained. This study compares the ability of four Lactobacillus plantarum strains from different niches to alleviate diarrhea caused by ETEC infection and explores their potential remission manner. The results showed that Lactobacillus plantarum CCFM1143 had the most obvious protective effect on diarrhea caused by ETEC. FGDLZ1M5, FCQNA30M6 and CCFM1143 reduced tumor necrosis factor-α (TNF-α), interferon-γ (IFN-γ) and interleukin (IL)-6 as well as jejunal injury. Moreover, FCQNA30M6 and CCFM1143 increased the aquaporin AQP3, and CCFM1143 increased interleukin (IL)-10 and decreased heat-stable enterotoxin (ST), while FGDLZ1M5 reduced the toll-like receptor (TLR4). The gut microbiota analysis demonstrated that ETEC increased Proteus and Pseudomonas and reduced Bifidobacterium, Odoribacter, Allobaculum and Blautia. A supplement of Lactobacillus plantarum could reconstruct the unbalanced gut microbiota. Furthermore, CCFM1143 significantly increased butyric acid, acetic acid, propionic acid and isobutyric acid, while FGDLZ1M5 only increased butyric acid. In summary, Lactobacillus plantarum alleviated ETEC-induced diarrhea by regulating the inflammatory cytokines, rebalancing the gut microbiota and modulating short-chain fatty acids (SCFAs) generation, which could provide the foundation and support for subsequent clinical trials and probiotic products.