Herein, pomegranate-like Silicon/Nitrogen-doped graphene microspheres (PSNGM) constructed by individual Si nanoparticle core wrapped by flexible nitrogen-doped reduced graphene oxide nanosheets (NG) have been synthesized through a facile and industrially large-scale spray drying approach. The PSNGM anode delivers excellent electrochemical performance: the reversible specific capacity at 100mAg−1 remains as large as 1141.6mAhg−1 after 150 cycles, with a high capacity retention of 96.1% from 2nd to 150th cycle; the capacity at 100mAg−1 can recover back to ∼1340mAhg−1 even after suffering a high current density of 5000mAg−1. The excellent performance is attributed to the unique pomegranate-like structure, nanoparticlization of Si and nitrogen doping of graphene: the pomegranate-like skeleton forms a highly conductive network, in which each Si nanoparticle is homogenously wrapped by flexible and conductive N-doped graphene nanosheets; flexible porous pomegranate-like structure can effectively accommodate the large volume variation during cycling; the N-doped graphene matrix guarantees its high conductivity for better electron and ion kinetics. The presented spray drying strategy is facile, low-cost and effective for large-scale industrial production of Si/graphene composite anode, and it can also be extended to fabricating other high-capacity electrode materials with low conductivities and large volume expansion.