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Previous studies on the early interference of gut microbiota by <i>Bacillus siamensis</i> (<i>B. siamensis</i>) in weaned piglets are rarely reported, and the present trial is a preliminary study. This experiment was conducted to investigate the effects of <i>B. siamensis</i> supplementation on the growth performance, serum biochemistry, immune response, fecal short-chain fatty acids and microbiota of weaned piglets. Sixty weaned piglets were randomly divided into a control group (CON) and a <i>B. siamensis</i> group (BS), which were fed a basal diet and the basal diet supplemented with 5 × 10¹⁰ CFU <i>B. siamensis</i> per kg, respectively. Each group had 3 replicates and 10 piglets per replicate. The trial lasted for 28 days. The results showed that <i>B. siamensis</i> significantly increased the serum growth hormone (GH) and insulin-like growth factor (IGF) in piglets. Compared with the CON group, the levels of serum immunoglobulin and inflammatory factors in the BS group were significantly improved. In addition, the serum concentrations of zonulin and endotoxin (ET) in the BS group were lower. The dietary addition of <i>B. siamensis</i> significantly increased fecal short-chain fatty acid (SCFA) levels in piglets. Notably, <i>B. siamensis</i> improved the microbial composition by increasing beneficial genera, including <i>Weissella</i>, <i>Lachnospiraceae_NK4A136_group</i> and <i>Bifidobacterium</i>, and decreasing pathogenic genera, including <i>Pantoea</i>, <i>Fusobacterium</i> and <i>Gemella</i>, in piglet feces. Correlation analysis showed that the benefits of dietary <i>B. siamensis</i> supplementation were closely related to its improved microbial composition. In summary, the addition of <i>B. siamensis</i> can improve the immunity function, inflammatory response, gut permeability and SCFA levels of weaned piglets, which may be achieved through the improvement of their microbiota.