BackgroundLeaves are the main medicinal organ inEpimediumherbs, and leaf flavonoid content is an important criterion ofEpimediumherbs. However, the underlying genes that regulate leaf size and flavonoid content are unclear, which limits the use of breeding forEpimediumdevelopment. This study focuses on QTL mapping of flavonoid and leaf-size related traits inEpimedium.ResultsWe constructed the first high-density genetic map (HDGM) using 109 F1 hybrids ofEpimedium leptorrhizumandEpimedium sagittatumover three years (2019–2021). Using 5,271 single nucleotide polymorphism (SNP) markers, an HDGM with an overall distance of 2,366.07 cM and a mean gap of 0.612 cM was generated by utilizing genotyping by sequencing (GBS) technology. Every year for three years, 46 stable quantitative trait loci (QTLs) for leaf size and flavonoid contents were discovered, including 31 stable loci for Epimedin C (EC), one stable locus for total flavone content (TFC), 12 stable loci for leaf length (LL), and two stable loci for leaf area (LA). For flavonoid content and leaf size, the phenotypic variance explained for these loci varied between 4.00 and 16.80% and 14.95 and 17.34%, respectively.ConclusionsForty-six stable QTLs for leaf size and flavonoid content traits were repeatedly detected over three years. The HDGM and stable QTLs are laying the basis for breeding and gene investigation inEpimediumand will contribute to accelerating the identification of desirable genotypes forEpimediumbreeding.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12870-023-04257-0.