Flexible electrochemical energy storage devices have attracted extensive attention as promising power sources for the ever-growing field of flexible and wearable electronic products. However, the rational design of a novel electrode structure with a good flexibility, high capacity, fast charge–discharge rate and long cycling lifetimes remains a long-standing challenge for developing next-generation flexible energy-storage materials. Herein, we develop a facile and general approach to three-dimensional (3D) interconnected porous nitrogen-doped graphene foam with encapsulated Ge quantum dot/nitrogen-doped graphene yolk-shell nano architecture for high specific reversible capacity (1,220 mAh g−1), long cycling capability (over 96% reversible capacity retention from the second to 1,000 cycles) and ultra-high rate performance (over 800 mAh g−1 at 40 C). This work paves a way to develop the 3D interconnected graphene-based high-capacity electrode material systems, particularly those that suffer from huge volume expansion, for the future development of high-performance flexible energy storage systems.