Abstract:[Background] Bacillus amyloliquefaciens BLCC1-0238 supplementation has been reported to effectively improve production performance and egg quality of laying hens in our previous study, the underlying mechanism, however, remains poorly understood. [Objective] The current study was conducted to examine the potential mechanism of B. amyloliquefaciens BLCC1-0238 to increase production performance of laying hens by evaluating cecal microflora and gene expression in ileum mucosa. [Methods] High-throughput sequencing technology was used to compare the differences of cecal microflora composition and gene transcription level of ileum mucosa between the basal diet group (group C) and B. amyloliquefaciens BLCC1-0238 supplementation group (0.06%, 2.0×1010 cfu/g, group T). [Results] B. amyloliquefaciens BLCC1-0238 supplementation can produce higher indexes of Chao1 and Shannon, which demonstrated increased diversity of cecal microflora. At the phylum level, the ratio of Firmicutes/Bacteroidetes was significantly increased, while relative abundances of Fusobacteria and Proteobacteria were reduced, and at the genus level, the relative abundances of Phascolarctobacterium, Lactobacillus, Ruminococcaceae UCG-014, Anaerotruncus, Ruminiclostridium 9, and Christensenellaceae_R-7_ group were all elevated, which indicated that B. amyloliquefaciens BLCC1-0238 supplementation altered the cecal microflora composition from different levels. With respect to gene expression change in ileum mucosa, 356 differentially expressed genes were identified, among which 199 genes were up-regulated and 157 genes were down-regulated. Bio-informatics analysis found that these up-regulated genes were involved in numerous signaling pathways associated with nutrition metabolism, such as glycine, serine and threonine metabolism, starch and sucrose metabolism, and galactose metabolism, which may accelerate nutrition absorption of laying hens. [Conclusion] B. amyloliquefaciens BLCC1-0238 supplementation can effectively improve laying hen production performance via increasing the diversity of cecal microflora and promoting nutrition absorption of laying hens, providing solid evidence for its further practical application.