Wheat is one of the most important cereal grain crops on the planet, and stomata is the key organ for photosynthesis and transpiration in plants. Stomatal conductance is determined by stomatal density and size, and regulating stomatal characteristics is essential for enhancing drought tolerance and agricultural water use efficiency. In this study, a set of 206 diverse common wheat varieties were genotyped by the wheat 660K SNP chip. The stomatal density and size of these materials grown in two environments were measured during the 2020-2021 growing season. Five single-locus GWAS models (MLM, CMLM, Blink, FarmCPU, MMLM) were performed for stomatal density and size to identify linked loci by R package Gapit. Combining the results of association analysis of each model, 67 high-confidence associated SNP loci (p<=1e-4) were identified, mostly on chromosomes 2A, 2B, and 4D. The markers AX-111137915, AX-108941269, and AX-110021982 on 2B showed a phenotypic interpretation rate (PVE) of roughly 10%. The haplotypes developed for four genes, TraesCS2B02G485400, TraesCS2B02G485500, TraesCS7A02G409200 and TraesCS7A02G410100, were able to classify the population into high and low stomatal density clusters, and these genes will be further validated. A large amount of loci correlated with stomatal density and size and advantage haplotypes of candidate genes will be useful to improving wheat stomatal traits for better drought resistance and water use efficiency.