This study endeavors to investigate the effects of Bifidobacterium breve CCFM1078 on bone formation and resorption balance in growing BALB/c mice. Newborn BALB/c mice were assigned to the control group (administration saline) and the CCFM1078 group (administration B. breve CCFM1078, 3 × 109 CFU/day) in 3-, 4-, and 5-week tests. All the groups have male and female distinctions. Our findings demonstrate that B. breve CCFM1078 exerts on the dynamic equilibrium between bone formation and resorption during the critical period of growth in mice by modulating the composition of gut microbiota and metabolites (hexadecanamide, linoleoyl ethanolamide, and palmitoyl ethanolamide), the genes and proteins expression related to the growth hormone (GH)/insulin-like growth factors-1 (IGF-1) axis and Gs/PKA/CREB signaling pathways, as well as downstream osteogenic and osteoclastic differentiation factors. The effects of B. breve CCFM1078 were different with age and gender dependent. This finding suggests B. breve CCFM1078 may have potential applications in regulating bone metabolism in the growth period population.