Horticultural crops are widely subjected to abiotic stresses such as extreme temperatures, waterlogging and high salinity, which not only seriously affect their growth and development, but also limit their adaptability and geographic distribution. Genome-wide association study (GWAS) is an effective approach developed in recent years to associate specific genetic variations with particular abiotic stress tolerance. Many causative allele(s)/loci have been identified using the power of this approach over the past decade. GWAS results can serve as a foundation experiment by providing insights into the genetic architecture of the trait, suggesting candidates for further functional study, and breeding new varieties with the gene pyramiding molecular design. In this review paper, we first provide the readers with the principle, characteristics and influencing factors of GWAS. Then, the applications of GWAS in studying of abiotic stresses in horticultural crops were presented in detail. We conclude this paper with important guidelines for better applications of GWAS in the further.