Chimeras are universal phenomena in the M₁-generation plants obtained following radiation-induced mutagenesis; however, the mutational effects and variant inheritance mechanisms of related rice chimeras have yet to be sufficiently clarified. In this study, we used target capture-seq technology to obtain OsNramp5 mutant chimeras via carbon ion beam irradiation, and used a 10 kb liquid chip to determine the SNP/InDel mutational occurrence and genetic isolation characteristics of the chimeric M₁ generation and mutational M₂ genomes. The results revealed that the mutation detected in the OsNramp5 gene of M₁ chimeric rice was not inherited by the M₂ generation; that is, the mutation detected in somatic cells of the M₁ population was not passed to the subsequent generation via the germ cells. In addition, conversion was established to be twice as common as transversion among the M₁ genomic mutation types, although more than half of the variant sites were inherited by the M₂ generation. However, these sites were rarely located within the functional coding regions of genes. Our findings in this study revealed the genomic variation characteristics of somatic M₁-generation chimeras induced by carbon ion beam irradiation and their genetic characteristics in the M₂ generation. These findings will provide a reference for further studies that seek to elucidate the mechanisms underlying chimeric mutation effects and for selecting appropriate procedures for mutagenesis breeding following carbon ion beam irradiation.