Scalable production of high-quality heteroatom-modified graphene is critical for microscale supercapacitors, but remains a great challenge. Herein, we demonstrate a scalable, single-step electrochemical exfoliation of graphite into highly solution-processable fluorine-modified graphene (FG), achieved in an aqueous fluorine-containing neutral electrolyte, for flexible and high-energy-density ionogel-based micro-supercapacitors (FG-MSCs). The electrochemically exfoliated FG nanosheets are characterized by atomic thinness, large lateral size (up to 12 um), a high yield of >70% with ≤3 layers, and a fluorine doping of 3 at%, allowing for large-scale production of FG-MSCs. Our ionogel-based FG-MSCs deliver high energy density of 59 mWh cm-3, by far outperforming the most reported MSCs. Furthermore, the all-solid-state microdevices offer exceptional cyclability with ~93% after 5000 cycles, robust mechanical flexibility with 100% of capacitance retention bended at 180°, and outstanding serial and parallel integration without the requirement of metal-based interconnects for high-voltage and high-capacitance output. Therefore, these FG-MSCs represent remarkable potential for electronics.