The development of digestive organs and the establishment of gut microbiota in pullets play an important role throughout life. This study was conducted to investigate the effects of Bacillus subtilis (BS) on growth performance, intestinal function and gut microbiota in pullets from 0 to 6 weeks of age. Hy-line Brown laying hens (1-day-old, n = 504) were randomly allotted into four diets with a 2 × 2 factorial design: (1) basal diet group (control); (2) antibiotics group (AGP), the basal diet supplemented with 20 mg/kg Bacitracin Zinc and 4 mg/kg Colistin Sulphate; (3) BS group, the basal diet supplemented with 500 mg/kg BS and (4) mixed group, the basal diet supplemented with both AGP and BS. As a result, when BS was considered the main effect, BS addition (1) reduced the feed conversion ratio at 4 to 6 weeks (P < 0.05); (2) decreased duodenal and jejunal crypt depth at 3 weeks; (3) increased the villus height : crypt depth (V : C) ratio in the duodenum at 3 weeks and jejunal villus height at 6 weeks and (4) increased sucrase mRNA expression in the duodenum at 3 weeks as well as the jejunum at 6 weeks, and jejunal maltase and aminopeptidase expression at 3 weeks. When AGP was considered the main effect, AGP supplementation (1) increased the V : C ratio in the ileum at 3 weeks of age; (2) increased sucrase mRNA expression in the duodenum at 3 weeks as well as the ileum at 6 weeks, and increased maltase expression in the ileum. The BS × AGP interaction was observed to affect average daily feed intake at 4 to 6 weeks, and duodenal sucrase and jejunal maltase expression at 3 weeks. Furthermore, dietary BS or AGP addition improved caecal microbial diversity at 3 weeks, and a BS × AGP interaction was observed (P < 0.05) for the Shannon and Simpson indexes. At the genus level, the relative abundance of Lactobacillus was found to be higher in the mixed group at 3 weeks and in the BS group at 6 weeks. Moreover, Anaerostipes, Dehalobacterium and Oscillospira were also found to be dominant genera in pullets with dietary BS addition. In conclusion, BS could improve intestinal morphology and change digestive enzyme relative expression and caecum microbiota, thereby increasing the efficiency of nutrient utilization. Our findings suggested that BS might have more beneficial effects than AGP in the study, which would provide theoretical evidence and new insight into BS application in layer pullets.