Constructing hybrids of transition metal oxides with different kinds of carbon based materials has attracted a lot of attention recently. However, scalable synthesis of homogeneous hybrids with active controllable of microstructure remains great challenge. Here, we proposed a convenient and efficient strategy named freeze-drying process for scalable production of 3D NiO/graphene hybrids. With a controllable procedure, NiO microflowers and graphene layers could preserve uniform configuration from fully mixed solvent to final hybrids materials. The mechanical stability and electrical conductivity of NiO microflowers was increased by graphene. NiO microflowers as spacers intercalated into graphene layers and effectively prevented it from aggregation or restacking, leading to a high specific surface area in hybrids. The NiO/graphene exhibited enhanced cycle stability and rate performance when evaluated as an anode for lithium ion batteries. It rendered high specific capacities about 1000mA h g−1 after 70 cycles, and 770mA h g−1 after 100 cycles at 300mAg−1. Excellent electrochemical properties were probably ascribed to the synergistic effect of NiO microflowers and graphene layers, as a result of smart structure design by a freeze-drying route. This strategy with merits of rational construction and scalable production could establish new aspects for diverse hybrid towards industrialization.