CRISPR technology enables precise modifications of DNA sequences in vivo and offers a great potential to harness plant genes for crop improvement and reshape global agriculture. To date, the majority of the reported editing events in crop plants were through error-prone non-homologous end joining (NHEJ) to generate gene knockouts. Enabling homology directed repair (HDR)-mediated gene replacement will have far more impactful applications, such as the introduction of elite alleles from local cultivars or the relative species into commercialized varieties, and targeted insertion of genes and/or regulatory elements at specific loci. Here, we successfully established CRISPR/Cas9-mediated genome editing system for targeted gene knock-out mutagenesis in rice and wheat, and generated multiple mutant lines for rice and wheat improvement. Furthermore, we established base-editing system through nCas9-cytidine deaminase fusion and gene replacement system through CRSISPR/Cas9-mediated H Moreover, we expanded the editing scope of LbCpf1 and obtained precisely edited rice plants using various resources of donor repair template through HDR by the newly developed CRISPR/Cpf1 system. Taken together, these results demonstrate that we can not only generate targeted mutagenesis for rice and wheat functional genomics and genetic improvement, but also precisely substitute single or several amino acid residues in proteins, or introduce an elite allele into commercial variety directly through CRISPR/Cas-mediated precise genome editing technologies, greatly expanding the ability to modify genes that confer agriculturally important traits in crop plants.