In this review, we focus on a small section of the literature that deals with the materials containing pristine defective carbon nanostructures (CNs) and those incorporated into the larger systems containing carbon atoms, heteroatoms, and inorganic components.. Briefly, we discuss only those topics that focus on structural defects related to introducing perturbation into the surface topology of the ideal lattice structure. The disorder in the crystal structure may vary in character, size, and location, which significantly modifies the physical and chemical properties of CNs or their hybrid combination. We focus mainly on the method using microwave (MW) irradiation, which is a powerful tool for synthesizing and modifying carbon-based solid materials due to its simplicity, the possibility of conducting the reaction in solvents and solid phases, and the presence of components of different chemical natures. Herein, we will emphasize the advantages of synthesis using MW-assisted heating and indicate the influence of the structure of the obtained materials on their physical and chemical properties. It is the first review paper that comprehensively summarizes research in the context of using MW-assisted heating to modify the structure of CNs, paying attention to its remarkable universality and simplicity. In the final part, we emphasize the role of MW-assisted heating in creating defects in CNs and the implications in designing their properties and applications. The presented review is a valuable source summarizing the achievements of scientists in this area of research.