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Probiotics have beneficial effects on improving egg quality, but there is little research about the effect of probiotics on metabolite composition, and the mechanisms are not yet fully understood. The aim of this study was to investigate the potential mechanisms by which compound Bacillusimproves egg quality and metabolite composition. A total of 20,000 Jingfen No. 6 laying hens at 381 d old were randomly divided into two treatments: control group with a basal diet, and the basal diet with compound Bacillussupplementation (Ba) group. The trial lasted eight weeks. The results showed that compound Bacillusimproved the gloss and strength of eggshells and reduced the ratio of sand-shell eggs by 23.8%. Specifically, the effective layer of eggshell was thicker and its calcite column was closely connected. Compound Bacillusincreased the contents of beneficial fatty acids in the egg yolk, and lipids and lipid-like molecules in the albumen (P< 0.01), while decreased the contents of total cholesterol, triglycerides, and benzene ring compounds in the egg yolk and organic oxygen compounds in the albumen (P< 0.01). In addition, the compound Bacillusincreased the calcium absorption in the duodenum by up-regulating the expression of transporters and serum hormone synergism (P< 0.05), and promoted metabolic balance of calcium and phosphorus. Simultaneously, uterine transcriptome showed that the expression of ChaC glutathione specific gamma-glutamylcyclotransferase 1 (CHAC1),glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1 (C1GALT1), phosphatidylinositol-4-phosphate 5-kinase type 1 beta (PIP5K1B), methylenetetrahydrofolate dehydrogenase 2 (MTHFD2), brain enriched myelin associated protein 1 (BCAS1), and squalene epoxidase (SQLE)genes were increased (P< 0.01), indicating that nutrient metabolism activity was enhanced. The expression of the BCAS1, C1GALT1,KLF transcription factor 13 (KLF13),and leucine rich repeat neuronal 1 (LRRN1) was increased (P< 0.01), indicating that the cell proliferation was enhanced, which slowed uterus aging. In conclusion, compound Bacillusimproved the eggshell strength and metabolite composition in the egg by promoting metabolic balance of calcium and phosphorus, cell proliferation, and nutrient metabolism in the uterus.