Background: Feed efficiency (FE) is a major determinant of productivity, economic sustainability, and environmental impact in livestock production. Although Pekin ducks constitute a substantial proportion of global poultry meat production, improvement of FE has progressed slowly, largely due to an incomplete understanding of its complex biological basis. In particular, how host genomic variation and gut microbial communities—especially across different intestinal segments—jointly contribute to FE remains poorly characterized in ducks. Results: We integrated whole-genome sequencing (WGS) with segment-resolved microbiota profiles from 313 Pekin ducks to delineate host–microbiota architecture underlying feed conversion ratio (FCR), which exhibited moderate heritability ( h ² =0.23, P _LRT = 2.53 × 10 ^–2 ). Genome-wide association study (GWAS) identified two major genomic regions involving two genes ALG13 and TRPC5 , which implicated in appetite regulation and energy balance to impact FE. Meanwhile, gut microbial communities exhibited spatial heterogeneity along the intestinal tract, with host genetics-associated taxa such as Solobacterium (cecum) and Eubacterium_eligens_group (jejunum) negatively correlating with FCR, likely via enhanced short-chain fatty acid production and improved energy harvest. Variation partitioning revealed that host genetics explained the largest FCR variance (36.96%), followed by cecal microbiota. Conclusions: Our results highlight coordinated host–microbiota interactions influencing FE, offering targets for breeding and microbiota-based interventions.