To investigate the impact of probiotics combined with yeast extract on the body composition and gut microbiome of female soccer players during routine training， a 42-day randomized， double-blind， placebo-controlled trial was conducted with 42 athletes. Body composition data and fecal samples were collected on days 0， 21， and 42 for metagenomic analysis. The results indicated significant increases in muscle mass in the lower left leg and upper right arm segments by 6.99% and 6.92% respectively at day 21， and a 5.48% increase in trunk bone mass， while the waist-to-hip ratio decreased by 4.13% at day 42 in the intervention group compared to the control group. Analysis of the gut microbiome revealed changes in microbial composition and function， characterized by increased abundance of beneficial bacteria such as Bifidobacterium animalis and Streptococcus salivarius， and decreased presence of potentially harmful bacteria like Haemophilus parainfluenzae and Roseburia faecis， along with reductions in phosphoglycerate mutase antibodies， prolyl-tRNA synthetase， and large subunit ribosomal proteins. Correlation analysis indicated that the combined supplement of probiotics and yeast extract enhanced trunk bone mass and reduced waist-to-hip ratios by modulating the abundance of Bifidobacterium animalis， increased upper right arm muscle mass through Streptococcus salivarius， and further reduced waist-to-hip ratios through the downregulation of small subunit ribosomal protein S13. These findings reveal the potential mechanisms by which probiotics and yeast extract regulate the stability of the gut microbiome to promote health in female soccer players and provide evidence-based support for the development of personalized microecological preparations.