Gut microbiota plays a crucial role in maintaining health and improving meat quality in broilers. In this study, an approach integrating quantitative metabolomics and metatranscriptomics was applied to investigate meat quality and gut microbiota in 90-day-old, 165-day-old, and 240-day-old Wuding chickens. The breast of 90-day-old broilers contained higher levels of amino acids (AAs) and small peptides, especially those contributing to umami flavor. Furthermore, multiple flavor substances that provide sweet flavor were observed to be more abundant in the breast of 90-day-old chicks. In contrast, 240-day-old broilers had higher contents of DPA and DHA in the breast. According to the analysis of meta-transcriptomics, the richness of active gut microbiota was found to be increased with the developmental trajectory, resulting in more complexity and stability of active gut microbiota in mature broilers. Comparison of the gene expression profiles in breast muscle indicated significant up-regulated genes related to the biosynthesis of AAs in 90-day-old chicks, which could contribute to higher levels of AAs and small peptides. Short-chain fatty acids were produced by active gut microbiota in mature broilers, which are associated with the more abundance of DPA and DHA in breast meat. This study represents a comprehensive effort to optimize broiler production through understanding the complex interplay between gut microbiology and meat quality.