Transposable elements (TEs) contribute to gene regulation and phenotypic diversity in plants. Miniature inverted-repeat TEs (MITEs) are short, non-autonomous DNA transposons that have been shown to be a major driver of gene expression changes, and we hypothesized that genome editing of MITEs might be an efficient approach to generate novel alleles with altered gene expression for tuning crop traits. Here, two agriculturally important rice genes, growth-regulating factor 4 (GRF4) and stress-responsive NAC1 (SNAC1), were selected for study. Using CRISPR/Cas9-mediated large-fragment deletion or insertion technology, we engineered the MITEs in the OsGRF4 and OsSNAC1 loci. A MITE deletion in the 3' UTR of OsGRF4 could increase the abundance of the target protein and improve many beneficial agronomic traits. A MITE insertion in the 5' UTR of OsSNAC1 could confer enhanced salt-inducible gene expression, thereby improving salt tolerance. In conclusion, we have shown that genetic engineering of MITEs in OsGRF4 and OsSNAC1 can create beneficial alleles for trait improvement in rice, providing a convenient and practical tool for crop breeding.