Improving resistance to Fusarium head blight (FHB) in wheat is crucial in the integrated management of the disease and prevention of deoxynivalenol (DON) contamination in grains. To identify novel sources of resistance, a genome-wide association study (GWAS) was performed using a panel of 213 accessions of elite wheat germplasm of China. The panel was evaluated for FHB severity in four environments and DON content in grains in two environments. High correlations across environments and high heritability were observed for FHB severity and DON content in grains. The panel was also genotyped with the 90K Illumina iSelect single nucleotide polymorphism (SNP) array and 11,461 SNP markers were obtained. The GWAS revealed a total of six and three loci significantly associated with resistance to fungal spread and DON accumulation in at least two environments, respectively. QFHB-2BL.1 tagged by IWB52433 and QFHB-3A tagged by IWB50548 were responsible for resistance to both fungal spread and DON accumulation. In summary, this study provided an overview of FHB resistance resources in elite Chinese wheat germplasm and identified novel resistance loci that could be used for wheat improvement.