Several epidemiological studies have suggested that flavonoid intake is associated with a decreased risk of cardiometabolic disease. However, the results remained inconsistent and there is no dose-response meta-analysis for specific outcomes. We conducted a meta-analysis to synthesize the knowledge about their associations and to explore their dose-response relationships. We comprehensively searched the PubMed, Embase, and Web of Science databases for prospective cohort studies published up to December 1, 2021. Summary relative risks (RR) and 95% confidence intervals (CI) were pooled for the association between flavonoid intake and cardiometabolic disease. Evaluations of linear or nonlinear dose-response were presented by restricted cubic splines. We identified 47 articles, including 1,346 676 participants and 127,507 cases in this meta-analysis. The summary of RR per 500 mg/d increase in flavonoid intake was 0.93 (95% CI 0.88–0.98) for cardiovascular disease, 0.89 (95% CI 0.84–0.94) for diabetes, and 0.97 (95% CI 0.94–0.99) for hypertension, respectively. We also found a linearity dose-response association between total flavonoid intake and cardiovascular disease (p nonlinearity = 0.541), and diabetes (p nonlinearity = 0.077). Our finding based on quantitative data suggested that a higher level of flavonoid intake is beneficial for the prevention of cardiometabolic diseases.