The present study investigated the influence of Bacillus subtilis GCB‐13‐001 on growth performance, nutrient digestibility, blood characteristics, faecal microbiota and faecal score in weanling pigs. A total of 120 weaning pigs [(Landrace × Yorkshire) × Duroc; 7.73 ± 0.75 kg (28 days of age)] were randomly allotted into three treatments according to their initial body weight (BW) and gender in a 6‐week experiment. There were 8 replication pens in each treatment, with five pigs/pen. Dietary treatment groups were as follows: (a) basal diet (CON), (b) CON + 0.1% Bacillus subtilis GCB‐13‐001 1 × 108 CFU/kg (T1) and (c) CON + 0.1% Bacillus subtilis GCB‐13‐001 1 × 109 CFU/kg (T2). Days 1 to 7, the BW and ADG with T2 treatment were higher (p < .05) than CON treatment, as well as F:G showed trends in linear reduction (p < .1). Days 8 to 21, the BW and ADG were improved (p < .05) in pigs offered T1 and T2 diets compared with CON diet. Days 22 to 42, BW and ADG were higher (p < .05) in pigs fed T2 diet than CON and T1 diets, and the pigs fed T1 diet had higher BW than CON treatment. Overall, the ADG with the T2 treatment was higher (p < .05) than that with the T1 and CON treatments, and pigs offered T1 treatment had higher (p < .05) ADG than CON treatment. Moreover, F:G ratio were significantly decreased (p < .05) by T2 treatment compared with CON treatment. The faecal Lactobacillus counts were improved, and E. coli counts were reduced (p < .05) in pigs fed T2 diet compared with CON at the end of the experiment. In conclusion, supplementation of 0.1% Bacillus subtilis GCB‐13‐001 1 × 109 CFU/kg has shown a beneficial effect in improving BW, increase ADG, decrease F:G ratio.