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<i>R2R3-MYB</i> represents a substantial gene family that plays diverse roles in plant development. In this study, 102 <i>SmR2R3-MYB</i> genes were identified from eggplant fruit and classified into 31 subfamilies. Analysis indicated that segmental duplication events played a pivotal role in the expansion of the <i>SmR2R3-MYB</i> gene family. Furthermore, the prediction of miRNAs targeting <i>SmR2R3-MYB</i> genes revealed that 60 <i>SmR2R3-MYBs</i> are targeted by 57 miRNAs, with specific miRNAs displaying varying numbers of target genes, providing valuable insights into the regulatory functions of miRNAs in plant growth, development, and responses to stress conditions. Through expression profile analysis under various treatment conditions, including low temperature (4 °C), plant hormone (ABA, Abscisic acid), and drought stress (PEG, Polyethylene glycol), diverse and complex regulatory mechanisms governing <i>SmR2R3-MYB</i> gene expression were elucidated. Notably, <i>EGP21875.1</i> and <i>EGP21874.1</i> exhibited upregulation in expression under all treatment conditions. Transcriptome and metabolome analyses demonstrated that, apart from anthocyanins (delphinidin-3-O-glucoside, cyanidin-3-O-(6-O-p-coumaroyl)-glucoside, and malvidin-3-O-(6-O-p-coumaroyl)-glucoside), overexpression of <i>SmMYB75</i> could also elevate the content of various beneficial compounds, such as flavonoids, phenolic acids, and terpenes, in eggplant pulp. This comprehensive study enhances our understanding of <i>SmR2R3-MYB</i> gene functions and provides a strong basis for further research on their roles in regulating anthocyanin synthesis and improving eggplant fruit quality.