Fusarium head blight (FHB) may cause serious losses in grain yield and quality under warm and humid conditions. Breeding for FHB-resistant cultivar is the most effective strategy for disease control. Chinese Spring-Sumai 3 7A substitution line (CS-SM3-7ASL) has a high level of FHB resistance, and a F7 population of recombinant inbred lines (RILs) was developed from the cross of CS-SM3-7ASL and Annong 8455. A genetic linkage map was constructed with 552 simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) markers and used for mapping of quantitative trait loci (QTLs) for FHB resistance. Two stable QTLs were detected over two years with one on 3BS that explained 27.0% and 38.6% of the phenotypic variance and another on 2D that explained 11.4 and 13.6% of the phenotypic variance. Additional QTLs were also detected on chromosiome 4A, 4D and 5A with one year's data. The FHB-resistance alleles of the QTLs on chromosome 2D, 3B and 4B were from CS-SM3-7ASL, whereas QTLs on chromosome 4A and 5A originated from susceptible cultivar Annong 8455. In addition, 13 epistatic loci on chromosome 1B, 1D, 2A, 2B, 4A, 4B, 5A, and 6B were also detected to have epistatic effects on the QTLs on chromosome 2D and 3B by using the conditional interaction search method. The result indicated that the FHB resistance in CS-SM3-7ASL is not from Sumai 3 chromosome 7A, but from QTLs and epistatic loci in Chinese Spring.