The gut microbiota plays a pivotal role in host metabolism, influencing the production of small metabolites from non-digestible compounds, which can accumulate in tissues and play important role in fatty acids synthesis for improving the meat quality. We investigate the breed-specific differences in longissimus dorsi (LD) muscle fatty acid profile, gut microbiota, and metabolites across the cecum, ileum, and rectum in Chinese Songliao Black pigs (SBP) and commercial Large White × Landrace crossbred pigs (LWLDP) and interactions. Significant correlations highlighting potential microbiota-metabolite interactions that contribute to muscle fatty acid composition. LWLDP pigs exhibited a higher number of significant fatty acids and maintained higher operational taxonomic units (OTUs) in the cecum and rectum, with no differences observed in the ileum between breeds. Firmicutes, Bacteroidetes, Proteobacteria, and Spirochaetes were the predominant phyla across both breeds. Differentially expressed metabolites (DEMs) were more abundant in the cecum and ileum of LWLDP, while rectum showed higher expression in SBP. Integrative analysis identified significant correlations between fatty acids, metabolites, and microbial taxa. DHA was linked to cecal metabolites and rectal microbial families, while saturated and unsaturated fatty acids were associated with different microbes and metabolites. This study demonstrates distinct breed-specific interactions between gut microbiota, metabolites, and fatty acid composition, offering insights into potential microbial interventions to enhance pork quality through fatty acid modulation.