The global prevalence of prediabetes is on the rise, and it is of value to manage prediabetes and predisposal to diabetes at an early stage. Myricetin is a natural polyhydroxyflavonoid, found in planta with several health benefits. This study aimed to evaluate the effects of myricetin on prediabetes. In vitro assay indicated that the cell viability, endocytosis and phagocytosis of macrophages were inhibited in RAW 264.7 cells under high glucose (HG) levels, concurrent with an increase in reactive oxygen species level. Administration of myricetin at a dose of 10 μM, restored the immunosuppressive effects mediated by HG. Moreover, the viability of Jurkat cells was also inhibited concurrent with inhibition of interleukin-2 (IL-2) and interferon-gamma (IFN-γ) expression levels versus increase PD-1 after treated with myricetin at the dose of 10 μM. In a prediabetic mouse model fed with high fat diet, increase in body weight, fat mass, fasting blood glucose, Triglyceride (TG), total cholesterol (TC) and low-density lipoprotein cholesterol (LDL-C) were observed. Flow cytometry analysis revealed a significant decrease in CD8+ T cells in the spleen and blood, whereas the expression of PD-1 on CD3+, CD4+, and CD8+ T cells in the spleen and lymph was significantly elevated. Administration of myricetin showed a potential hypoglycemic and lipid-lowering effect in both prevention and treatment, in addition to restoration of innate and adaptive immune immunity in mice and confirmed by the in vitro immunomodulation effect. In addition, 16S rRNA showed that myricetin ameliorated prediabetes may be related to decrease in the relative abundance of Acetatifactor, Blautia, Intestinimonas, Anaerotruncus, and Peptococcus.