Zinc selenide (ZnSe) is a next-generation anode material due to its high sodium storage capacity. However, the poor conductivity and volume expansion lead to its capacity attenuation and short cycle life. Herein, Se-vacancy porous ultrathin ZnSe nanosheet/carbon composite (ZnSe@NC/N-GQD) is reported as a high-performance anode material for sodium-ion batteries. Organic-inorganic hybrid ZnSe(en)0.5 ultrathin nanosheets with abundant Se vacancies are rapidly prepared by electron beam irradiation for the first time. Using it as a precursor, Se-vacancy carbon-coated porous ultrathin ZnSe nanosheets loaded with nitrogen-doped graphene quantum dots (N-GQDs) are synthesized via carbonization and electrodeposition process. Through the design of ZnSe@NC/N-GQD, the sodium storage performance can be effectively improved by implementing nanostructure engineering (porous ultrathin nanosheet) via organic–inorganic hybrid, defect engineering (Se vacancy) via electron beam irradiation, and carbon composite (amorphous carbon and N-GQD). Consequently, ZnSe@NC/N-GQD delivers a high capacity of 483 mA h g−1 after 200 cycles at 0.5 A g−1, shows an outstanding rate capability of 381 mA h g−1 at 10.0 A g−1, and exhibits an excellent cycling stability of 86 % retention after 2800 cycles at 5.0 A g−1. This work develops a new method to rapidly prepare organic–inorganic nanohybrids, and proposes an innovative design of high-performance ZnSe-based anodes.