Glucose metabolism plays an important role in many normal and pathological physiological processes in the body. The breakdown and synthesis of muscle glycogen provides ATP for muscle activities. A genome-wide association study for muscle glycogen was performed in 473 Jingxing yellow chickens to identify significant single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs) involved in muscle glycogen metabolism. A total of nine SNPs ( < 1/699341) and three INDELs ( < 1/755733) reached a significant level of potential association. The following results were obtained through a series of analyses, including additive effects and gene function annotation. Two significant SNPs were found in introns 12 and 13 of copine 4 () on chromosome 2. The wild-type and mutant individuals had significant differences in glycogen metabolism at two loci ( < 0.01 for both). Individuals carrying two mutations had increased muscle glycogen content. According to the gene annotation of chromosome 11, there is a significant INDEL in intron 6 of naked cuticle homolog 1 (). After the INDEL mutation, the glycogen content increased significantly. There was a significant difference between wild-type and mutant individuals ( < 0.01). These mutations likely affecting two genes ( and ) may affect glycogen storage in a pleiotropic manner. Gene annotation indicates that and may affect the process of glucose metabolism. Our findings contribute to understanding the genetic regulation of muscle glycogen metabolism and provide theoretical support.