Micronutrient malnutrition is the most common public health problem in the world. Biofortification is the most attractive and sustainable solution to alleviate micronutrient deficiency in humans, which requires the development of new crop varieties with higher concentrations of zinc (Zn) and iron (Fe) in edible parts. In this study, a recombinant inbred line (RIL) population derived from two modern wheat cultivars Zhongmai 175 and Xiaoyan 60, was used to identify quantitative trait loci (QTL) for grain Zn concentrations (GZnC), grain Fe concentrations (GFeC) and thousand kernel weight (TKW). A total of 16 QTL including 6 for GZnC, 6 for GFeC and 4 for TKW were identifed. The six QTL for GZnC located on chromosomes 2DL, 4BS, 5AS, 5DL, 6A and 6DL, respectively, and explained 2.0%-24.0% of the phenotypic variances; six QTL for GFeC on 1DL, 2DL, 3BS, 3DL, 4BS and 6A, contributed to 1.7%-28.6% of phenotypic variation; and four QTL for TKW on 2DL, 3DL, 4BS and 6A, accounted for 4.0-30.2% of phenotypic variation. The QTL on 2DL, 4BS, and 6A were simultaneously associated with GZnC, GFeC and TKW in a synergistic manner. The 2DL QTL located on a 26.8 Mb suppressed recombination region which hinders the map-based cloning of the causative gene. The QTL was further validated in Zhongmai 175/Lunxuan 987 RIL population by its tightly linked Kompetitive Allele Specific PCR (KASP) markers K-AX-109500250. A glutamine synthetase (GS) gene TaGS2-2D (TraesCS2D02G500600, 595.1 Mb) related to the increase of nitrogen uptake and TKW was identified as a potential candidate. The 4BS and 6A QTL increased plant height and were likely the wide type of Rht-B1 and Rht25, respectively. This study explored the possibility of synergistically improving GZnC, GFeC and TKW, and provided valuable loci and markers for wheat biofortification.