Grain size and morphology is one of the main factors that determine the wheat yield, it is of great significance to mine the associated loci of grain size and morphology related traits and screen related candidate genes for improving wheat yield. In this study, 300 representative natural populations of winter wheat at domestic and exotic excellent were used as research materials to identify the phenotype of 9 grain traits, including 1000-grain weight, grain length, grain width, grain thickness, grain length-width ratio, grain area, grain perimeter, grain shape and grain plumpness. Wheat genotypes were collected by 90 K SNP chip, and genome-wide association study of grain size and morphological traits was carried out by mixed linear model (MLM+Q+K).The results showed that the traits related to grain size and morphology showed rich phenotypic variation, the coefficient of variation ranged from 3.80%~-26.06% and the broad heritability was 56.25%~-91.89%. 66 stable association loci (P ≤ 0.001) related to grain size and morphology were detected by GWAS, which were distributed on 18 chromosomes except 3D, 4D and 5D, which could explain 3.74%~-14.34% of phenotypic variation. for pleiotropic loci associated with two or more grain traits we detected 37. among which the BS00022512_51 marker detected on chromosome 3B was simultaneously correlated with 4 grain traits (grain length, grain width, grain thickness and grain length-width ratio), with the largest apparent contribution rate (7.06%~-14.34%), the wsnp_Ex_c4480_8055475 markers detected on chromosome 6D were simultaneously associated with six grain traits except grain thickness, grain shape and grain plumpness, and the phenotypic contribution rate was 3.81%-8.25%. Haplotype analysis of BS00022512_51 and wsnp_Ex_c4480_8055475 markers showed that there were three haplotypes of GC-Hap1, AT-Hap2 and AC-Hap3 in wsnp_Ex_c4480_8055475 markers loucs on chromosome 6D, and Haplotype GC-Hap1 is a haplotype with large grains and high 1000-grain weight. The distribution frequencies of the three haplotypes were 65.58% and 32.25% and 2.17%, respectively. Haplotype GC-Hap1 was widely selected in four winter wheat regions in China. Nine candidate genes were proposed based on 37 significantly-associated multiple effect SNPs.