Plant height is an important agronomic trait that affects wheat yield. To identify new genetic loci that are significantly associated to plant height, the genome-wide association study (GWAS) was conducted using 152 newly introduced synthetic wheat lines from International Maize and Wheat Improvement Center (CIMMYT). This population was subjected for measuring plant height at three environments and genotyping using 55K single nucleotide polymorphism (SNP) chip. The plant height was observed with a a normal distribution in synthetic genotypes, with the mean value of 97.9 cm, which was higher than that of modern cultivars (70.5 cm) but lower than that of local landraces (114.8 cm) in Huanghuai zone. Analysis of variance showed significant differences in the plant height of synthetic wheat in genotype, environment and interaction between environment and genotype. 37916 markers were qualified using filtering parameters to be polymorphic including 14404, 14566 and 8946 SNPs on the A, B and D sub-genome respectively. Population structure analysis of 152 synthetic wheat lines suggested three groups. GWAS using the mixed liner model (MLM) on the best linear unbiased prediction values (BLUP) revealed 24 significant SNPs (P≤0.0001), which were found on chromosomes 1A, 3B, 4A, 4B, 4D, 5A, 5B, 6A, 6D and 7B, each explaining12.33%-20.1% of the phenotypic variation. The annotation in a physical interval of 3 Mb querying significant SNPs suggested a total of 669 genes, among which 131 genes were found highly expressed in wheat stems or leaves (TPM≥5) in public transcriptome data. According to the functional annotation of wheat gene models and rice gene homologs, we speculated that five genes were possibly involved in plant height development. Since these significant loci did not overlap with previously reported QTLs, they may represent new genetic loci in controlling plant height. Collectively, these results provided new germplasm and selection markers in order to improve plant height in wheat.