The F2 mapping population including 202 lines derived from the cross between “578” (large grain) and “Sanfensan” (small grain) were used in present study. A genetic linkage map covering 21 linkage groups (LG) was created with 172 SSR markers. The method of CIM was used to detect QTLs related with grain traits. A total of 17 QTLs were identified, of which 6 for grain length (GL) explaining 0.7%-12.83% of the phenotypic variation, 5 for grain width (GW) explaining 0.77%-12.92% of the phenotypic variation, 6 for 1000-grain weight (TGW) explaining 0.58%-10.64% of the phenotypic variation. Four QTLs with over 10% contribution to phenotypic variation were considered as major genes, i.e. qGL-2 (12.83%) for grain length, qGW-5 (12.92%) for grain width, qTGW-3 (10.64) and qTGW-4 (10.05). It is interested that qGL-2 and qTGW-4 are located the same location of the linkage group. In addition, we detected that the interval between AM1089 and AM1512 on linkage group 3 was associated with the grain length, grain width and 1000-grain weight. Meanwhile, the interval between AM1044 and AM939 on linkage group 3 was related to the grain length and 1000-grain weight, and the interval between AM3217 and AM965 was relative with the grain width and 1000-grain weight. The outputs of this research pave the way for studying in oat grain traits and developing marker assistant selection for naked oats.