Diversity surveys of germplasm are important for gaining insight into the genomic basis for crop improvement, especially InDels, which are poorly understood in hexaploid common wheat. Here, we described a map of 89,923 InDels from exome sequencing of 262 accessions of a Chinese wheat mini-core collection. Population structure analysis, principal component analysis and selective sweep analysis between landraces and cultivars were performed. Further genome-wide association study (GWAS) identified five QTLs that were associated with spike length. Two loci on chromosomes 2B and 6A about 12.5 Mb were detected in ten environments. Assisted with RNA-seq data, we identified 14 and 21 genes respectively that expressed in spike and rachis within the two QTL regions that can be further investigated for candidate genes discovery. Moreover, InDels were found to be associated with awn lengths on chromosomes 5A, 6B, and 4A, which overlapped with previously reported genetic loci B1 (Tipped 1), B2 (Tipped 2), and Hd (Hooded). One of the genes TaAGL6 that was previously shown to affect floral organ development was found at the B2 locus to affect awn length development. Our study shows that trait-associated InDels may contribute to wheat improvement and may be valuable molecular markers for future wheat breeding.