Abstract Trogtalite CoSe 2 nanobuds encapsulated into boron and nitrogen codoped graphene (BCN) nanotubes (CoSe 2 @BCN‐750) are synthesized via a concurrent thermal decomposition and selenization processes. The CoSe 2 @BCN‐750 nanotubes deliver an excellent storage capacity of 580 mA h g −1 at current density of 100 mA g −1 at 100th cycle, as the anode of a sodium ion battery. The CoSe 2 @BCN‐750 nanotubes exhibit a significant rate capability (100–2000 mA g −1 current density) and high stability (almost 98% storage retention after 4000 cycles at large current density of 8000 mA g −1 ). The reasons for these excellent storage properties are illuminated by theoretical calculations of the relevant models, and various possible Na + ion storage sites are identified through first‐principles calculations. These results demonstrate that the insertion of heteroatoms, B–C, N–C as well as CoSe 2 , into BCN tubes, enables the observed excellent adsorption energy of Na + ions in high energy storage devices, which supports the experimental results.