Fusarium crown rot (FCR) is a severity and chronic disease in common wheat and could result in serious yield loss as well as health problems to livestock and people. Here, 243 Chinese wheat cultivars from 4 different environments were investigated for FCR resistance and were further performed genome-wide association studies using the wheat 660K genotyping assay. The results indicated that most cultivars surveyed showed FCR disease index (DI) of 40-60, and some cultivars showed stable FCR resistance (DI < 30). GWAS analysis indicated that a total of 286 SNPs was identified to be significantly associated with FCR resistance. Of them, 266, 6 and 8 were distributed on chromosomes 6A, 6B and 6D. Further analysis of the significant SNPs on 6A showed that they ranged in 7.1 Mb containing 53 annotated genes. Physical mapping showed that there were 3 FCR-resistant QTLs, and the QTLs QFCR.hau-6A with the PVE of 7.77-10.17%, QFCR.hau-2D with the PVE of 7.15-9.29% and QFCR.hau-2A with the PVE of 5.24-6.92% could be detected in 4, 3 and 3 environments. Combination of GWAS and QTL mapping showed that the QFCR.hau-6A was the most significant QTL to modulate FCR resistance in this study and should be paid more attention to use for improvement of FCR resistance. These results could provide valuable FCR-resistant germplasms and markers in wheat breeding program and could also provide useful information for understanding molecular and genetic basis of FCR resistance in common wheat.