Coleoptile length, in wheat, is a significant agronomic trait impacting yield by facilitating the successful establishment of seedlings. In arid regions, varieties possessing longer coleoptile can evade harsh conditions by deep sowing, paving the way for improved yield. However, the study of genes involved in coleoptile development is insufficient. In this study, a high-density 660 K SNP array was used for genome-wide association study (GWAS) on coleoptile length in 150 wheat varieties. The findings revealed the detection of 353 significantly associated SNPs across all environments. The integration of linkage disequilibrium analysis and haplotype analysis mined 23 core QTLs capable responsible for the stable regulating coleoptile length in wheat. In wheat varieties characterized by extended coleoptile length, 6,600, 11,524, and 6,059 genes were found to be differentially expressed at three distinct developmental stages within the coleoptile, respectively. Through GWAS, gene expression levels, and functional annotation, we concluded the identification of two candidate genes (TraesCS2B02G423500, TraesCS2B02G449200) regulating wheat coleoptile length. By employing WGCNA and protein interactions prediction, discovered that the 19 genes were found to interact with candidate genes and participate in plant hormone metabolism and signaling, cell elongation or proliferation, which collectively contributing to coleoptile elongation. Additionally, two KASP markers were developed which can be used in breeding. These results offer a basis for understanding the genetic regulatory network responsible for wheat coleoptile length formation. The QTLs and candidate genes identified in this study can be further utilized for genetic improvement of wheat coleoptile length.The online version contains supplementary material available at 10.1007/s11032-024-01520-6.