The heartwood of Rhus verniciflua Stokes (Anacardiaceae) is widely used for a medicinal plant to treat diabetes mellitus and lingering intoxication in the folkloric society of Korea, while the stem bark has been traditionally used to treat menstrual disorder and helminthiasis. We previously reported that a flavonoid, fustin, isolated from the heartwood of R. verniciflua is effective in Alzheimer‘s disease and rheumatoid arthritis. To explore the possibility to produce more flavonoid-rich fraction from this plant, the MeOH extracts from the plant parts of stem bark, outer heartwood, and inner heartwood were quantitatively analyzed by HPLC. Phenolic or flavonoid compounds (chlorogenic acid, caffeic acid, p-coumaric acid, sulfuretin, fustin, fisetin, luteolin and astragalin) were detectable in the HPLC chromatogram. The orange-colored inner heartwood was found to contain the highest levels of fustin (16.96 mg/g) and sulfuretin (2.22 mg/g). Moreover, the inner heartwood accumulated fustin and sulfuretin at least 4-fold higher level as compared to the stem bark and outer heartwood. The levels of total phenolic compounds positively correlated with the extents of antioxidant properties. Therefore, the inner heartwood of R. verniciflua could be used to increase fustin concentration of the extract which is capable of treating Alzheimer‘s disease and rheumatoid arthritis.