Defect engineering has been a core strategy for promoting the electrochemical properties. Herein, the multiple defects, which consist of oxygen vacancies and cation vacancies caused by Fe3+ substitution, have been introduced into the VO2(B)-based nanomaterials as an effective protocol to boost their electrochemical performance. A series of ternary compounds of Fex-VO2(B) (x = 0, 0.005, 0.010, 0.030 and 0.050) has been prepared by one-step hydrothermal methods combined with annealing. The morphology, the crystal structure and bond environments of the Fex-VO2(B) have been carefully examined. The Fex-VO2(B) (x = 0.005) electrode exhibits the capacity of 137.5 F·g− 1 at a current density of 1 A·g− 1 and an appreciable 81.1% capacity retention after 1000 cycles at 0.1 A·g− 1. Meantime, the coin cells have been assembled and deliver a 282.37 mAh·g− 1 at 0.1 A·g− 1. The enhancement of the electrochemical performance can be elucidated as the cooperative effects of cation vacancies and oxygen vacancies coupled with the lattice shrinkage by the Fe3+ substitution into the VO2 structure.