Mutation induced by irradiation is one of the efficient ways to innovate crop germplasm resources. In this study, a drooping-panicled mutant rice with other variations in the panicle, named JD-1, was derived from ‘Jindao 565’ by carbon ion beam irradiation. Compared with the agronomic traits of the wild type ‘Jindao 565’, JD-1 had a highly significant (P＜0.01) increase in neck-panicle curvature, number and density of main panicle grains by 305.90%, 66.86% and 47.79%, respectively. In addition, panicle length, number of main panicle filled grains and number of main panicle secondary branches increased significantly (P＜0.05) by 12.11%, 63.06% and 74.19%, respectively, but the 1000-grain weight significantly decreased by 11.54%. The whole genome sequence alignment revealed the existence of 18639 single nucleotide polymorphisms (SNPs) with a conversion/transversion ratio of 2.34, and of 3428 insertion-deletions (InDels), between ‘Jindao 565’ and JD-1, which were distributed in clusters and mainly located on chromosomes 5 and 11, accounting for 25.19% and 22.98%, respectively. Through the structural analysis of mutated genes, the mutations occurred in intergenetic regions had the maximum proportion of 45.22%, while those detected in splicing hold the minimum proportion of 0.08%. GO functional analysis of the mutated genes revealed that most of them were involved in cell physiological process. The sixteen genes related to plant height, 1000-grain weight, panicle length and secondary branches were identified from the cloned genes which were mutated in JD-1. The molecular markers for these genes were further designed based on the mutation sites, and the twelve SNP markers and the nine InDel markers were proved to be polymorphic in nine genes between ‘Jindao 565’ and JD-1. This study created a new rice germplasm and explored the allelic variation related to yield trait in rice.