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To assess the effects of MYB genes on total flavonoid content and flavonoid component content in Cerasus humilis fruits, members of the MYB gene family were identified and analyzed based on C. humilis genomic data and using bioinformatics. In total, 223 ChMYB genes were identified. According to the Myb DNA-binding domain, the 223 ChMYB genes were divided into four groups, i.e., 1R, R2R3, 3R, and 4R, comprising 112, 106, 4, and 1 ChMYB genes, respectively. The ChMYB genes were distributed unevenly on eight chromosomes, and some large replication fragments were observed. Promoter analysis showed that ChMYB genes play an important role in hormone responses and regulation of flavonoid biosynthesis. According to the transcriptome data and qRT-PCR analysis, several ChMYB genes may play an important role in different tissues such as leaf, seed, and fruit tissue and during fruit development. We tested correlations between expression levels of different genes and the content of total flavonoids and flavonoid components, resulting in three important ChMYB genes which were closely associated with the content of flavonoid components. The relative expression levels of ChMYB1 and ChMYB117 were strongly associated with the content of catechin and quercetin-7-O-β-D-glucopyranoside, respectively, and ChMYB52 was strongly associated with the change in peel color. We identified several potential candidate genes that regulate the synthesis of C. humilis flavonoids. Our results provide comprehensive insights into the functions of ChMYB family genes and may constitute a foundation for gene function verification in the future; after knowing the effect of ChMYB on flavonoid synthesis of C. humilis, we can accelerate the breeding of C. humilis with high flavonoid content by transgenic technology. [ABSTRACT FROM AUTHOR]