A weight-related QTL was found in the 15 linkage group (LG) during mapping the growth traits of grass carp (Ctenopharyngodon idella). And we tried to screen insert/deletion mutations on three scaffolds in the 15 LG, according to the previous consensus linkage map and draft genome of C. idella. At the meantime, the STR genotyping method was uesed in genotyping of insert/deletion mutations. Moreover, the association analysis of selected mutations and growth traits of 323 individuals was conducted. Results found that 17 of the 44 selected insert/deletion mutations were SSRs, and 2 loci failed to design primers; therefore, 25 pairs of primer were successfully designed. PCR amplifications showed that only 22 of the 25 primer pairs were effective. Then STR genotyping method was used for genotyping of those 22 insert/deletion mutations, and 7 polymorphic mutations were found in four parents. Afterwards, PCR products were sequenced to confirm the STR genotyping results. Sequencing results showed that STR genotyping method could not only classify insertion/deletion mutants accurately, but also reduce the genotyping costs. Finally, the general linear model was used to analyze the relevance between those 7 insert/deletion mutations and growth traits of 323 juvenile C. idella. Correlation results found that 2 loci (ID-10H and ID-41F) were not related with growth traits, while the other 5 loci were significantly related with one or more growth traits of juvenile C. idella. According to the 5 loci, locus ID-6H was significantly correlated with fatness traits of juvenile C. idella, while locus ID-11F, ID-15F, ID-32F and ID-39F were significantly correlated with body weight or length or width or height. In summary, the inexpensive STR genotyping method could be used in the development of insert/deletion mutations, and the 5 growth related mutations could be used in QTL density-increasing and molecular marker assisted breeding of C. idella.