Horticultural crops are widely subjected to abiotic stress conditions such as extreme temperatures, waterlogging and high salinity. The harsh conditions seriously destabilize their growth and development and limit their adaptability and geographic distribution. Genome-wide association study (GWAS) is an effective approach by associating the genetic variations with the phenotypic variations. Over the past decade many genetic loci/genes have been identified by using the power of this approach. GWAS results can serve as a foundation for deciphering the genetic architecture and identifying candidate genes for functional study, and breeding new varieties via gene pyramiding. In this review we represent the principle, characteristics and influencing factors of GWAS, its application in studying of abiotic stresses in horticultural crops, as well as the prospective for exploring the functional genes in future.