Graphene is a potential energy storage material for supercapacitor electrodes because of its unique electronic and physical properties. In this study, graphene was functionalized chemically. The functionalized graphene (G) is an ideal substrate for anchoring MnO2 nanoflower (NF) through controlled electrodeposition to improve the performance of supercapacitors. The controlled weight ratio of functionalized graphene and MnO2 NF is 1:8. The G/MnO2 NF electrodes exhibit excellent electrochemical performance with a high specific capacitance of 320.59 F g−1 at a current density of 0.5 A g−1 and excellent cycling stability with 95.5% capacitance retention over 3000 cycles. Symmetric supercapacitors with G/MnO2 NF hybrid materials were also assembled as electrodes. The cells exert promising characteristics with a specific capacitance of 55.37 F g−1 at a scan rate of 5 mV s−1, maximum energy density of 5.67 Wh kg−1, and power density of 5.11 kW kg−1. The facile and low-cost preparation technique of functionalized graphene and high-performance G/MnO2 NF nanocomposites may provide a new paradigm for fabricating supercapacitors with superior performance.