Block copolymer self-assembly is a widely used technique for obtaining many interesting nanostructures. The development of efficient and rapid processes for driving block copolymer self-assembly has remained a challenge. Microwave heating has attracted much attention in bioenergy production and in the food industry due to the advantages associated with dielectric heating effects. We report here a simple method (like microwave cooking) of microwave-heating-induced microphase separation of a carbohydrate-based block copolymer, maltoheptaose-block-polystyrene (MH-b-PS). Highly ordered and perpendicularly orientated MH cylinders of 7 nm diameter were formed in the PS matrix on a bare silicon wafer after annealing at 333 K for 1 s. The whole process is performed at a relatively low temperature undernbvvl atm, and no solvent is needed during the process. The mechanism of this method is investigated by using the grazing-incidence small-angle X-ray scatting technique to make a detailed comparison with the conventional thermal annealing process. MH-b-PS cannot achieve self-assembly by conventional thermal annealing. In contrast, microwave energy can transfer directly to the polar MH blocks in the MH-b-PS thin films, which helps MH-b-PS self-assemble quickly. This study circumvents a major barrier to using carbohydrate-based block copolymer materials.