Wheat kernel color related traits L*, a*, and b* are important indicators of wheat quality. In order to reveal the genetic loci that regulate wheat kernel color related traits, we investigated phenotypes of L*, a*, and b* in a natural population that composed of 243 wheat accessions in Huanghuai wheat region in four environments, and characterized the population by the wheat 660K SNP assay. Furtherly, genome-wide association studies (GWAS) was performed for wheat kernel color related traits. Results indicated that, 785 significant SNP associated with kernel color traits were identified, explaining 11.4%~23.4% phenotypic variation. SNP associated with L* are mainly distributed on chromosome 1A and 2B; SNP associated with a* are mainly distributed on chromosome 2A, 2B, 2D, 4B, 5B, 5D, 7A, and 7D; SNP associated with b* are mainly distributed on chromosome 2B, 5B, 5D, 7A, 7B, and 7D. Of them, 51 SNP were pleiotropic. Further, a total of 36 potential candidate genes related to the kernel color traits were identified by gene annotation. Only 8 of the 36 potential candidate genes are expressed in the kernel, including the known gene Pinb. Furtherly, gene polymorphism analysis showed that Pinb and UDP-glucose/GDP-mannose dehydrogenase gene TraesCS5B02G399800 were significantly associated with the target traits. Differential haplotypes of TraesCS5B02G399800 were detected significantly associated with b* by haplotype analysis. Therefore, this study provided a reference for marker-assisted selection and whole genomic prediction for wheat kernel color traits.