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Antibiotic-associated diarrhea (AAD) refers to diarrhea caused by gut microbiota disorders after the use of antibiotics, which seriously threatens the health of humans and animals. Therefore, it is necessary to find an effective therapy to treat AAD. This research aimed to explore the effects of <i>Lactobacillus plantarum</i> H-6 (<i>L. plantarum</i> H-6) and <i>Weissella viridescens</i> J-1 (<i>W. viridescens J-1</i>) on alleviating antibiotic-associated diarrhea induced by lincomycin hydrochloride (LH) in mice. The results show that <i>L. plantarum</i> H-6 could significantly reduce the expression of pro-inflammatory factors such as <i>IL-1β</i> and <i>IL-6</i> in colon tissue. At the same time, <i>L. plantarum</i> H-6 significantly increased the abundance of <i>Lactobacillus</i> and <i>Akkermansia</i>, decreased the abundance of <i>Bacteroides</i>, and increased the contents of L-tryptophan, LysoPC (20:4 (8Z, 11Z, 14Z, 17Z)), reduced riboflavin, threoninyl–methionine, and N-palmitoyl in serum. However, <i>W. viridescens</i> J-1 had little effect on the treatment of AAD. It can be concluded that <i>L. plantarum</i> H-6 can regulate mice’s colonic microbial composition, improve their serum metabolic process, and alleviate antibiotic-associated diarrhea. This research may provide a novel therapeutic option for AAD.