In recent years, wheat fusarium crown rot(FCR)has been seriously appeared in many wheat regions of China, and posing a great threat to grain production. In addition, many toxins and secondary metabolites such as DON and NIV were produced during the disease occurrence, which brought serious problems to food safety and human or animal health. As the effort of current research mainly focuses on the isolation of FCR pathogens and the investigation of materials resistance, the progress of FCR study is far behind the speed of disease development. Therefore, it is of great significance to screen excellent resistant resources to control this disease. This study used millet grains as pathogen medium to inoculate the 163 wheat germplasm accessions in the Huanghuai valley of China. The results showed that there were no immune or highly resistant materials have been identified, but the resistance level estimated by disease index (DI) of the identified accessions was obvious difference with a normal distribution from 10.27 to 83.33. The correlation coefficient between seedling and field investigation results was 0.79 which indicated a highly correlation of seedling resistance to adult resistance. Furthermore, the genome-wide association study (GWAS) results showed that the significant SNPs were widely distributed on all the wheat chromosomes, and mainly focus on 2A with an interval from 725 Mb to 763Mb. The bulked segregant analysis (BSA) results suggested that the significant SNPs were mainly distributed from 730 Mb to 750Mb on 2A. Overall, the GWAS and BSA analysis indicated that a significant resistance locus on chromosome 2A from 730 Mb to 750Mb was identified to associate with FCR infection. This study can provide important reference for resistant materials investigation and resistance loci excavation on wheat FCR.