Although defect engineering is widely reported in catalysis, the influence of defects on electrochemical performance is less reported and the defect-related electrochemical mechanism is not fully understood. In this work, the oxygen vacancy concentration is controlled simply by calcining different precursors. The Co3O4 samples by prepared cobalt-thiourea coordination and cobalt nitrate precursors are named as S1 and S2, respectively. It is found that cobalt-thiourea coordination compound can provide an oxygen-rich skeleton, thus reducing oxygen vacancy; the specific capacitance of S1 (79.5 F/g) is 12.5 times higher than that of S2 (5.9 F/g) at 0.2 A/g. The remarkably improved capacitance is mainly attributed to the appropriate amount of oxygen vacancy for S1. Theory calculations confirm that an appropriate concentration of oxygen vacancy favors the desorption of K+ and the adsorption of OH–, and the kinetics of surface redox reaction; while excessive oxygen vacancies are disadvantageous to the electrochemical process. Additionally, the S1-based asymmetric supercapacitor (ASC) displays a high energy density of 176 μWh/cm3, a high power density of 218 mW/cm3, and a long cycling life (72.6% capacitance retention after 2500 charge/discharge cycles). The ASC is so flexible that it can be easily assembled in series to drive a light-emitting diode to work. This work provides a simple, low-cost method for producing high-quality electrode materials on a large scale.