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.