Genome-wide association study (GWAS) has become a widely accepted strategy for decoding genotypephenotype associations in many species thanks to advances in next-generation sequencing (NGS) technologies.Maize is an ideal crop for GWAS and significant progress has been made in the last decade.This review summarizes current GWAS efforts in maize functional genomics research and discusses future prospects in the omics era.The general goal of GWAS is to link genotypic variations to corresponding differences in phenotype using the most appropriate statistical model in a given population.The current review also presents perspectives for optimizing GWAS design and analysis.GWAS analysis of data from RNA,protein,and metabolite-based omics studies is discussed,along with new models and new population designs that will identify causes of phenotypic variation that have been hidden to date.The joint and continuous efforts of the whole community will enhance our understanding of maize quantitative traits and boost crop molecular breeding designs.