In this paper, a novel approach for controlling the direction of defect evolution in graphene through intercalation of organic small molecules into graphite oxide (GO) combined with a one-pot microwave-assisted reaction is reported. By using ethanol as intercalator, the bulk production of high quality graphene with its defects being satisfactorily healed is achieved. The repair of defects using extraneous carbon atoms and the hybrid state of these carbon atoms are definitely demonstrated using isotopic tracing studies with (13)C-labeled ethanol combined with (13)C solid-state NMR. The defect healed graphene shows excellent crystallinity, extremely low oxygen content (C : O ratio of 23.8) and has the highest sheet conductivity (61 500 S m(-1)) compared to all other reported graphene products derived from GO. By using methanol or benzene as intercalators, hierarchically porous graphene with a self-supported 3-dimensional framework (∼917 m(2) g(-1)) containing both macropores and mesopores (2-5 nm) is obtained. This graphene possesses a distinctive amorphous carbon structure around the edge of the nanopores, which could be conducive to enhancing the lithium storage performance (up to 580 mA h g(-1) after 300 cycles) when tested as an anode of lithium ion batteries, and might have promising applications in the field of electrode materials, catalysis, and separation, and so on. The mechanism involved for the controlled defect evolution is also proposed. The simple, ultrafast and unified strategy developed in this research provides a practical and effective approach to harness structural defects in graphene-based materials, which could also be expanded for designing and preparing other ordered carbon materials with specific structures.