Wheat is one of the main food crops in the world and an important source of trace elements in human body. Copper (Cu) and manganese (Mn) are essential trace element in human growth. However, the lack of trace nutrition elements caused by malnutrition affects more than 2 billion people around the world, therefore, it is the significance for the development and utilization of excellent germplasm resources to screen germplasm resources rich in trace elements, explore the excellent alleles controlling the content of trace elements in grains, and clarify the genetic mechanism of their related traits. 23,536 high-quality DArT markers were used to map quantitative trait loci (QTL) for grain Cu (GCu) and grain Mn (GMn) concentrations in 164 F6 recombinant inbred lines (RILs) from Avocet/Chilero. A total of 7 QTL loci were detected on chromosome 2B, 4A, 4B, 5B, 5D, 6B, 7B and 7D, respectively. Among them, two major QTLs for GCu and three major QTLs for GMn were identified, temporarily named as QGCu.haust-4BS, QGCu.haust-7DS, QGMn.haust-6BS, QGMn.haust-7BL and QGMn.haust-7DS, which could explain 11.48%-23.60% of the phenotypic variation. The closely linked molecular markers were 1124059, 3950570, 100006031, 1056704, 100168640, SNP2260263, SNP1143330, SNP1230343, 1260330 and 3954697, respectively. One stable QTL was detected in multiple environments, QGCu.haust-4AL, respectively, which could explain 2.58%-11.84% of the phenotypic variation. QGCu.haust-4AL was closely linked to SNP100512195 and 1721210, with genetic distances of 0.26 cM and 5.79 cM, respectively, with physical location is between 720.1 and 731.0 Mb. According to the above analysis. The selected excellent germplasm resources rich in trace elements, the five major QTL loci located developed with them can be used for the selection of trace elements, established a theoretical foundation for marker-assisted selection and biofortification molecular breeding.