Transition metal dichalcogenides exhibit several different phases (e.g., semiconducting 2H, metallic 1T, 1T′) arising from the collective and sluggish atomic displacements rooted in the charge-lattice interaction. The coexistence of multiphase in a single sheet enables ubiquitous heterophase and inhomogeneous charge distribution. Herein, by combining the first-principles calculations and experimental investigations, a strong charge transfer ability at the heterophase boundary of molybdenum disulfide (MoS₂) assembled together with graphene is reported. By modulating the phase composition in MoS₂, the performance of the nanohybrid for energy storage can be modulated, whereby remarkable gravimetric and volumetric capacitances of 272 F g⁻¹ and 685 F cm⁻³ are demonstrated. As a proof of concept for energy application, a flexible solid-state asymmetric supercapacitor is constructed with the MoS₂-graphene heterolayers, which shows superb energy and power densities (46.3 mWh cm⁻³ and 3.013 W cm⁻³, respectively). The present work demonstrates a new pathway for efficient charge flow and application in energy storage by engineering the phase boundary and interface in 2D materials of transition metal dichalcogenides.