Display omitted •We report one concept for synthesis of atomically dispersed RuO2-graphene quantum dot-graphene.•Ultrasmall RuO2 was atomically dispersed on graphene sheets with a very high Ru loading of 4.2%•The intimate contacts achieve to formation of double Schottky heterojunctions at the interfaces.•Ru in hybrid brings an increased capacitance of more than five times of the theoretical value of RuO2.•The study offers one way for synthesis of graphene-based composites with high catalytic activity. Poor capacity and cycle stability limit many applications of supercapacitors in wearable electronic devices. The study reports synthesis of atomically dispersed RuO2 (AD-RuO2)-tryptophan functionalized graphene quantum dot (Trp-GQD)-graphene (G) hybrid. Trp-GQD was bound to graphene oxide (GO) by π-π stacking and then combined with Ru3+ ion via Ru-N coordination bond to form Ru-Trp-GQD-GO complex. Followed by partial reduction into graphene gel with hydrazine hydrate, thermal reduction in N2 and oxidation in air in sequence. The resulting AD-RuO2-Trp-GQD-G offers well-defined three-dimensional structure and high Ru loading of 4.2%. RuO2 was atomically dispersed on the graphene sheets. The intimate contacts of Trp-GQD with G and RuO2 create the double Schottky heterojunctions at the interfaces and results in an excellent catalytic activity. The AD-RuO2-Trp-GQD-G electrode exhibits high capacitance of 503.7F g−1 at 1 A g−1. The value is much higher than that of graphene electrode (160F g−1) and G-Trp-GQD electrode (192F g−1). This verifies that the introduction of Ru per gram can bring an increased capacitance of 7421.4F, which is more than five times of the theoretical value of RuO2 electrode. The flexible supercapacitor displays high capacitance (354F g−1 at 0.5 A g−1), rate-capacity (186F g−1 at 20 A g−1) and cycling stability (99.6% capacity retention after 10,000 cycles at 10 A g−1). The supercapacitor is able to deliver a power density of up to 52000 W kg−1 and energy density of up to 332 Wh Kg−1 and good application prospect in wearable electronic devices.