The InDel markers have been widely used in the research fields of molecular marker-assisted breeding of fruit trees. However, there are few reports on the related studies of Chinese traditional characteristic fruit trees “Chinese bayberry”. In this study, a total of 25,831 InDels with a size distribution ranging from 1 to 50 bp were obtained through whole genome resequencing and bioinformatics analysis of 103 Chinese bayberry core germplasm. The frequency of InDel variation on different chromosomes ranged from 8,903 to 11,297bp. Among them, the frequency of InDel mutation was the highest on chromosome CM025856.1. Annotation analysis showed that 1,312 InDels were distributed in the gene exon region, and another 21,055 and 6,659 InDels were distributed in the intergenic region and intron region, respectively. Through GO annotation, the functions of the above InDels molecules mainly include binding and catalytic activity. Biological processes mainly involve cellular processes and metabolic processes. KEGG pathway analysis showed that the function of InDels gene region was mainly include secondary metabolism, carbon metabolism and nucleocytoplasmic transport. The results of genome-wide association analysis were used to obtain 20 InDels that were significantly associated with riping-stage traits of Chinese bayberry fruits. Their functional annotations mainly involved mitochondria, plastid structural genes, riboside triphosphate hydrolase and cytokinin signaling proteins. Further verification and analysis screened out the InDel EP-18 labeled Chinese bayberry fruit maturity traits identification accuracy was higher, up to 89.25%; Through gene prediction results, it was found that this locus annotation was an Early nodulin family gene. In conclusion, InDel EP-18 markers obtained in this study will provide an important theoretical basis for molecular assisted breeding of Chinese bayberry.