Abstract1T‐MoSe2 is recognized as a promising anode material for sodium‐ion batteries, thanks to its excellent electrical conductivity and large interlayer distance. However, its inherent thermodynamic instability often presents unparalleled challenges in phase control and stabilization. Here, a molecular intercalation strategy is developed to synthesize thermally stable 1T‐rich MoSe2, covalently bonded to an intercalated carbon layer (1TR/2H‐MoSe2@C). Density functional theory calculations uncover that the introduced ethylene glycol molecules not only serve as electron donors, inducing a reorganization of Mo 4d orbitals, but also as sacrificial guest materials that generate a conductive carbon layer. Furthermore, the C─Se/C─O─Mo bonds encourage strong interfacial electronic coupling, and the carbon layer prevents the restacking of MoSe2, regulating the maximum 1T phase to an impressive 80.3%. Consequently, the 1TR/2H‐MoSe2@C exhibits an extraordinary rate capacity of 326 mAh g−1 at 5 A g−1 and maintains a long‐term cycle stability up to 1500 cycles, with a capacity of 365 mAh g−1 at 2 A g−1. Additionally, the full cell delivers an appealing energy output of 194 Wh kg−1 at 208 W kg−1, with a capacity retention of 87.3% over 200 cycles. These findings contribute valuable insights toward the development of innovative transition metal dichalcogenides for next‐generation energy storage technologies.