Polyploid heterosis is a common phenomenon in plant kingdom and has been noted for more than a century. Common wheat (Triticum aestivum, AABBDD) is not only an important food crop, but also a model plant for studying PpH. In this work, we constructed a high-quality reference genome for the modern leading variety Aikang 58 (AK58) and established a comprehensive genomic database. Comparisons between AK58 and the landrace Chinese Spring (CS) revealed the variations in genome structure and gene expression that played primary roles in wheat improvement. We found that subgenome diploidization and divergence were essential and crucial for PpH. Hence, we proposed homoeologous GWAS (HGWAS) to detect PpH loci in common wheat. A total of 123 major PpH loci were detected including well-known and new gene loci for wheat improvement. We suggest Vrn1, a major PpH gene detected here, as a candidate new Green Revolution gene; its superior homoeoallele haplotypes (HHs) not only contributed to yield increase in the past but may also significantly enhance wheat yield potential in the future. Systematic analysis of HHs should be an effective way to reveal more elite PpH loci for enriching gene diversities valuable for wheat improvement. The HGWAS approach can be applied to detect PpH loci in all polyploid crops, thus representing a breakthrough in PpH exploitation and utilization.