Considerable efforts have been devoted to developing sodium-ion batteries for large-scale energy storage due to the high abundance and low cost of sodium resources. However, the inferior cyclability and reaction kinetics of electrodes toward sodium ions still impedes their further development. In this study, we designed a two-dimensional (2D) composite where ultrafine CoSe nano-crystallites were confined in N-doped carbon (CoSe/NC-L) to attain excellent cycling performance and fast sodium ion storage. The CoSe/NC-L was successfully prepared through a high-temperature reaction of leaf-like Co-based ZIF (ZIF-L) and Se powder. It is demonstrated that the particle size of Se powder plays an important role in the formation of ultrafine CoSe nano-crystallites and encapsulated configuration. The combined merits of ultrafine CoSe and encapsulation into 2D NC matrix effectively enhance reaction kinetics, accommodate volume change expansion of CoSe and inhibit the formation of unstable SEI. Therefore, the CoSe/NC-L composite displayed high initial specific capacity of 530 mAh g−1 and Coulombic efficiency of 67.2% at 0.2 A g−1. Notably, superior capacity retention of 82.2% with stable Coulombic efficiency of 97.0% is achieved at 0.5 A g−1 after 150 cycles in NaClO4 electrolyte system. This work casts a new light on the smart design of metal selenide electrode materials for sodium ions batteries.