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Simple Summary: Most Chinese local breeds have slow growth speed and high fat deposition, while European commercial chicken strains belong to fast-growing chicken breeds with low fat deposition. In general, the word "You" in China represents excessive fat deposition, and You-chicken is considered to be a typical fatten broiler. Among more than 100 local chickens in China, Baicheng-You and Beijing-You chickens are only two kinds of You-chicken breeds. However, their special genomic characteristics have not been well studied. This study analyzed the genome changes among these chicken breeds and obtained many candidate genes related to important traits of chickens, e.g., fat deposition, immune response, and melanin production. Our data provide valuable insights for understanding the formation of germplasm characteristics of these broiler breeds, which can be used to better protect and utilize the Chinese-You chickens. As the only two You-chicken breeds in China, Baicheng-You (BCY) and Beijing-You (BJY) chickens are famous for their good meat quality. However, so far, the molecular basis of germplasm of the two You-chicken breeds is not yet clear. The genetic relationship among BCY, BJY, and European-origin broilers (BRs) was analyzed using whole genome resequencing data to contribute to this issue. A total of 18,852,372 single nucleotide polymorphisms (SNPs) were obtained in this study. After quality control, 8,207,242 SNPs were applied to subsequent analysis. The data indicated that BJY chickens possessed distant distance with BRs (genetic differentiation coefficient (FST) = 0.1681) and BCY (FST = 0.1231), respectively, while BCY and BRs had a closer relationship (FST = 0.0946). In addition, by using FST, cross-population extended haplotype homozygosity (XP-EHH), and cross-population composite likelihood ratio (XP-CLR) methods, we found 374 selected genes between BJY and BRs chickens and 279 selected genes between BCY and BJY chickens, respectively, which contained a number of important candidates or genetic variations associated with feather growth and fat deposition of BJY chickens and potential disease resistance of BCY chickens. Our study demonstrates a genome-wide view of genetic diversity and differentiation among BCY, BJY, and BRs. These results may provide useful information on a molecular basis related to the special characteristics of these broiler breeds, thus enabling us to better understand the formation mechanism of Chinese-You chickens. [ABSTRACT FROM AUTHOR]