QTLs of three milling yield traits, including brown rice (BR,%), milled rice (MR,%) and head milled rice (HR,%), were mapped using a set of 212 Lemont/Teqing RI population, an RFLP linkage map with 182 markers and a mixed model approach(QTLMapper V1.0). The population showed continuous distributions with transgressive segregation on both sides for all traits while HR had a wider variation than BR and MR. One and four main effect QTLs were detected for MR and HR. Two QTLs for HR(QHr6 and QHr7) had large additive effects. Twelve, five and sixteen pairs of digenic epistatic loci were associated with BR, MR and HR respectively. Epistasis was more important than main effect QTLs according to the mapping result. A complex relationship was observed for epistatic pairs mapped in same trait or among different traits by sharing intervals.