The late rearing stage is a critical period for the development of body weight and body size traits in chickens. In this study, we investigated the genetic architecture underlying these traits in 925 healthy 16-week-old Wenshang Barred chickens, with the aim of identifying candidate genes and genetic markers for trait improvement. We performed a genome-wide association study, linkage disequilibrium analysis, genotype–phenotype effect analysis, and enrichment analysis for body weight and seven body size traits. Heritability estimates for these traits ranged from 0.18 to 0.48. The study identified 89 candidate genes, including SETDB2, CAB39L, RB1, TRIM13, LDB2, and LCORL. In addition to the classic growth-associated region at GGA4:72.48–76.42 Mb, we identified an important region at GGA4:68.24–70.22 Mb, located approximately 2.3 Mb upstream, as well as an important region at GGA1:168.03–170.24 Mb. Functional enrichment analysis revealed that candidate genes were nominally enriched (p < 0.05) in amino sugar and nucleotide sugar metabolism, biosynthesis of nucleotide sugars, calcium signaling, and neuroactive ligand–receptor interaction pathways. Collectively, our findings clarify the genetic basis of body weight and body size traits during the late rearing stage and may provide a basis for further evaluation of genetic markers in indigenous chicken breeding programs.