Purpose of this letter was to explore the trends regarding methodological flaws of systematic review and meta-analyses (SRMAs) based on retraction notes in the past decades, and the categories of reasons for the retractions. Content analysis with descriptive statistics, Cochran Q test, and multinomial logistic regression were used. Based on 187 records of retracted SRMAs, retraction announcements can be categorized into academic ethical violation, methodological flaw, and writing or reporting problem. The numbers of academic ethical violation were significantly higher than those with methodological flaw (z = 3.51; p < 0.01) or writing problem (z = 8.58; p < 0.001). The numbers of methodological flaw were also higher than that with writing problem (z = 6.47; p < 0.001). Moreover, an increased proportion of methodological flaw was observed since 2006, and the retraction year was significantly associated with increased proportion of methodological flaw when academic ethical violation as the reference group.