The rational strategy to design the well-ordered morphology of the metal oxides with defective engineering and tailoring them into specific electrode fabrication can significantly improve their electrochemical properties for high-performance energy storage systems. Herein, we adopted an effective strategy to introduce oxygen-defect into the well-ordered three-dimensional flower-like CoMoO4 nanoarchitecture. The Co-Mo precursor leads to the introduction of oxygen-defects into the CoMoO4 (rCMO) nanoarchitecture during the heat-treatment under an oxygen-controlled environment (argon). The oxygen-defects in the material could facilitate abundant electroactive sites and intrinsically enhance the conductivity and supercapacitor performance. The oxygen-defect CoMoO4 (rCMO) exhibits a specific capacity of 531 mAh g−1 at a current density of 1 A g−1 compared to the pristine CoMoO4 (CMO; ambient atmosphere) of 322 mAh g−1 under the same current density. Meanwhile, the fabricated hybrid supercapacitor (HSC) of rCMO//AC provides a maximum specific capacitance of 159 F g−1. Further, it distributes an energy density of 49.87 Wh kg−1 at the power density of 845.45 W kg−1 with an excellent cyclic life of ~91.03% over 10 000 cycles.