Hierarchical structural [email protected]2 nanocomposite is synthesized via a facile electrochemical co-deposition of the intercalation of PEDOT into flower-like MoS2 microspheres. The SEM, TEM, and other characterization results demonstrate the hierarchical [email protected]2 composite with an enlarged interlayer spacing of MoS2 to 1.02 nm, in which PEDOT nanoparticles act as intercalation, and flower-like MoS2 microspheres are used as a substrate for growth. The electrochemical characterizations indicate that the [email protected]2 electrode has an ultra-high specific capacitance of 4418 mF cm−2 at 2 mA cm−2 and remarkable cycling stability, retaining 100% of the initial capacitance at a high current density of 100 mA cm−2 after 10,000 cycles. The symmetric [email protected]2 supercapacitor presents a high energy density of 88.3 mWh cm−2 at 60 mW cm−2, and outstanding cycling stability (93% after 10,000 cycles). These prominent electrochemical performances are attributed to the expanded interlayer spacing, the synergistic effect between PEDOT and MoS2, the low resistance, along with the [email protected]2 porous structure, indicating great potential applications of the [email protected]2 electrode in the energy storage field.