3D multilayer graphene anode materials have shown great potential for energy storage devices due to their extraordinary structural stability combined with unique electrochemical characteristics. Herein, a facile strategy is proposed to synthesize 3D multilayer graphene nanostructures (M-GNS, M refers to graphitization catalyst) via microwave catalytic graphitization incorporated with liquid oxidation and thermal reduction using biomass-based activated carbon. The role of various graphitization catalysts on the characteristics and lithium storage performance of GNS were systematically investigated. Transmission electron microscopy results show that the use of Co led to the formation of multilayer graphene nanostructures with lower thickness compared to Ni and Fe. Various characterization techniques showed that the degree of graphitization in Co-graphitized activated carbon was lower, and the sample was dominated by smaller graphitic structures. When used as lithium-ion battery anode material, Co-GNS delivered superior rate capability (357 mAhg−1 at 5 Ag−1 after 1000 cycles with a capacity retention of ~94 %), and ultrahigh charge capacity (1695 mAhg−1 at 0.1 Ag−1), mainly owing to its thinner multilayer nanostructure.