To meet the pressing needs of fast development of energy and environmental science, sodium ion batteries (SIBs) are considered as the promising novel generation of power storage system, due to abundant reserves and low price of sodium sources. In this work, N-doped C-encapsulated scale-like yolk-shell structured MoSe2-C materials assembled by expanded (002) planes few-layer MoSe2 nanosheets are successfully synthesized by a facile general strategy. The few-layer crystal fringes are no more than 4 layers. Notably, the interlayer spacing of (002) planes is expanded to 1.15 nm, which is larger than its intrinsic value of pristine MoSe2 (0.64 nm). Particularly, the few-layer nanosheets with expanded (002) planes are spaced-restricted growing in the inner wall and the surface of hollow carbon frame and form scale-like yolk-shell hybrid MoSe2-C structure. When evaluated as anode for SIBs, the MoSe2-C materials show ultra-long cycling life, maintaining 378 mA h g−1 over 1000 cycles at 3 A g−1. It also exhibits outstanding rate capability and the Coulombic efficiencies for all the rate performance reaching more than 98.3% except the first one. The expanded (002) planes, 2D fewer-layer nanosheets and unique N-doped C-encapsulated scale-like yolk-shell frame are responsible for the enhanced electrochemical performance.