Three-dimensional (3D) graphene networks are performance boosters for functional nanostructures in energy-related fields. Although tremendous intriguing nanostructures-decorated 3D graphene networks have been realized, on-demand decoration of nanostructures in the specified position of interest within the whole 3D graphene skeleton is still out of reach, shedding limitations on constructing more sophisticated components with programmable structures which offer enormous potential for the enhancement of performance and exploration of new functions. Here, we report the melamine-sponge (MS)-templated hydrothermal method capable of realizing reduced graphene oxide (RGO)-nanostructure composite aerogels with programmable structures and compositions. The key of this method is using the MS template to preset the structures of choice through programmable solution-processed immobilization of graphene oxide (GO) and nanostructures. Remarkably, the hydrothermal treatment simultaneously removed the MS template and reduced the GO networks without changing the preset structures. We showcased nine typical RGO-nanostructures composite aerogels to demonstrate the versatility of the MS-templated hydrothermal method.