Developing efficient non-precious materials as bifunctional catalysts for both oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) is very urgent for the practical application of the regenerative fuel cells. Herein, a hydrothermal-assisted defect engineering is introduced as an efficient strategy to enhance the electro-catalytic performance of spinel Co3O4 nanostructures without complex chemical treatments. By simply tuning the hydrothermal time, we fabricate a typical cubic Co3O4 nanostructure with high density of oxygen vacancy defects. The formation of the surface oxygen vacancies is measured by XPS, Raman spectroscopy, and TG/DTA measurements. The relative concentration of oxygen vacancies could reach 8.5 at% for the cubic oxide fabricated at a hydrothermal time of 3 h. In 1 M NaOH electrolyte, the cubic Co3O4 displays improved both ORR and OER activity with a total overpotential of 783 mV, which is close to that obtained by commercial Pt/C or RuO2 catalysts. The enhanced performance should be attributed to the increased oxygen vacancy defects as well as the desired Co2+/Co3+ ratio for the cubic oxide. This work may offer a possibility for developing other spinel oxides with high performance through hydrothermal-assisted defect engineering.