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Heteroatom doping is an effective way to generate oxygen vacancies and improve the electrochemical properties of materials. However, the heteroatom doping process is more complicated and it is difficult to ensure the simultaneous generation of defects. In this work, TiO2 quantum dots/graphene aerogel composites were synthesized via a simple hydrothermal method. The N and S atoms were successfully incorporated by electron beam irradiation, and a large number of defects were introduced. The effects of irradiation dose on the doping amount, elemental morphology, and electrochemical properties of the compounds were further studied. The synergistic effect between graphene’s double-layer capacitance and TiO2 quantum dots’ pseudocapacitance, as well as the introduction of heteroatomic doping and defects, is beneficial to improve the electrochemical performance of the material. When used as an electrode material for supercapacitors, NT-NSG-140 at an irradiation dose of 140 kGy shows the best electrochemical performance. At a high current density of 5 A g–1, the NT-NSG-140 maintains a capacity of 127.8 F g–1. This work provides an environmentally friendly, simple, and efficient method for designing high-performance materials containing heteroatoms.