Common wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) is one of the most important staple crops in the world. Despite the fact that wheat production has significantly increased over the past decades, it is still facing unprecedented challenges in the context of global climate changes, increasing world population, decreased farm land resources and water shortages in arid and semi-arid lands. The hexaploidy nature and gene redundancy of wheat make a forward genetics approach to select a desired phenotype, very time-consuming and in some cases impossible because of gene linkage or drag. To ensure global food and ecosystem security, there is an urgent need to resilience wheat production and minimize environmental pollution by using the cutting-edge technologies. CRISPR/Cas9 technology enables precise modifications of DNA sequences in vivo and offers a great promise for harnessing plant genes for crop genetic improvement. However, wheat genome editing lag behind other food crops due to its complex genome and polyploidy nature, as well as relatively low transformation efficiency. Here, we successfully generated multiple wheat mutant lines high in resistant starch, increased nitrogen use efficiency and yield potential, and improved disease resistance, respectively, through CRISPR/Cas9-mediated genome editing of diverse agronomic important genes such as SBEIIa related to the synthesis of amylopectin, ARE1 orthologs related to nitrogen use efficiency, TaJAV1 related to sheath blight resistance and Fhb1 related to Fusarium head blight (FHB) resistance in wheat. Besides, we developed an efficient CRISPR/Cas9 multiplexing system by using polycistronic tRNA strategy to simultaneously produce multiple sgRNAs. We demonstrated the simultaneous editing of two, three, four and five genes at up to 15 genomic loci in an elite wheat variety by multiplex gene editing. Following embryo rescue and segregation, we successfully recovered transgene-free plants with targeted mutagenesis at up to 15 genomic loci and pyramided the favorable alleles in an elite wheat variety in one generation. The established single and multiplex gene editing system here would greatly facilitate fundamental biological research and translational breeding process in hexaploidy wheat as well as in other agriculturally important polyploid crop species for sustainable agriculture development.