Boron-graphdiyne (BGDY), which has a unique π-conjugated structure comprising an sp-hybridized carbon skeleton and evenlydistributed boron heteroatoms in a well-organized 2D molecular plane, is prepared through a bottom-up synthetic strategy. Excellent conductivity, a relatively low band gap and a packing mode of the planar BGDY are observed. Notably, the unusual bonding environment of the all sp-carbon framework and the electron-deficient boron centers generates affinity to metal atoms, and thus provides extra binding sites. Furthermore, the expanded molecule pores of the BGDY molecular plane can also facilitate the transfer of metal ions in the perpendicular direction. The practical effect of the all sp-carbon structure and boron heteroatoms on the properties of BGDY are demonstrated in its performance as the anode in sodium-ion batteries.