Molybdenum disulfide (MoS2) has shown potential as a supercapacitor electrode material, owing to its high theoretical specific capacitance and wide negative potential window, especially in neutral electrolytes. However, its practical application is hindered by low inherent electrical conductivity and narrow interlayer spacing. In this study, oxygen-incorporated MoS2 nanoflowers with 1T/2H hybrid phase were fabricated on a graphite foil substrate (1T/2H-O-MoS2@GF) from molybdenum blue solution via a facile hydrothermal process. Dispersible Mo-blue clusters, composed of polymerized structures containing numerous MoOx-type building units combined with NH4+ cations, were formed by introducing ammonium persulfate before hydrothermal synthesis; they were subsequently used as precursors of MoS2. Mo-blue clusters lead to the formation of metallic 1T-phase dominant heterostructure and incorporation of oxygens in MoS2 during the hydrothermal reaction. The 1T/2H hybrid phase formed by using Mo-blue clusters provided MoS2 with excellent stability in the 2H-phase and high electrical conductivity in the 1T-phase, simultaneously. The incorporated oxygens induced a wide interlayer spacing (9.8 Å) and improved the surface hydrophilicity of MoS2, thereby facilitating the fast diffusion of electrolyte ions. As a result, the 1T/2H-O-MoS2@GF electrode exhibited a high specific capacitance of 280 F g−1 at 1.0 A g−1 and 88% capacitance retention after 10,000 cycles at 10 A g−1. The asymmetric supercapacitor device, assembled using a 1T/2H-O-MoS2@GF negative electrode and MnO2@GF positive electrode, demonstrated superior power and energy densities of 450–18000 W kg−1 and 39.7–5.46 Wh kg−1 in a working window of 1.8 V.