Epidemiological studies evaluating the association of flavonoids intake with risk of coronary heart disease (CHD) have produced inconsistent results. We conducted a meta-analysis to summarize the evidence from prospective cohort studies regarding the association between flavonoids intake and risk of CHD. Pertinent studies were identified by searching Web of Knowledge, Pubmed and Wan Fang Med Online up to April 2014. Fixed-effect or random-effect model was used to combine the results based on the heterogeneity. Dose-response relationship was assessed by restricted cubic spline. Publication bias was estimated using Begg' funnel plot and Egger's regression asymmetry test. Fourteen articles with 15 prospective studies involving 7,233 CHD cases and 452,564 participants were included in this meta-analysis. Pooled results suggested that highest flavonoids intake versus lowest intake was significantly associated with the risk of CHD [summary relative risk (RR) = 0.850, 95% confidence interval (CI) = 0.794-0.910, I(2) = 26.0%, τ(2) = 0.041]. Inverse associations were found both in Europe and in USA. Linear dose-response relationship was found between flavonoids intake and CHD risk. However, no significant association was found through the dose-response analysis (an increment of 20 mg/day, summary incidence rate ratios (IRR) = 0.95, 95%CI = 0.88-1.02). Our results from this meta-analysis suggested that elevated flavonoids intake might have a protective effect on CHD.