The performances of beryllium-doped graphdiyne (GDY) as an anode material for lithium-ion batteries at various doping sites are investigated by first-principles methods based on density functional theory. Calculations of the formation and cohesive energies of GDY at different doping concentrations indicate that beryllium-doped GDY has excellent prospects for experimental synthesis. More importantly, the beryllium-doped GDY exhibits good electrical conductivity. The adsorption energy for a single lithium atom on beryllium-doped GDY is -4.22 eV, which is significantly higher than that of boron, nitrogen-doped GDY, and intrinsic GDY. As the number of stored lithium atoms increases, the adsorption energy remains greater than the cohesive energy of solid lithium, and the average open-circuit voltage stays between 0-1 V, ensuring the safety of the battery. Additionally, the lithium storage capacity is increased to 881 mAh/g, which is 1.14 times that of undoped GDY and 2.36 times that of graphite. Meanwhile, the diffusion performance of lithium on beryllium-doped GDY is also enhanced. For the C _IIIsite doping system, by studying the ion transport at low, medium, and high lithium concentrations, we find that as the lithium concentration increases, the diffusion barriers are 0.38, 0.44, and 0.77 eV, respectively, making lithium ion movement more difficult, but still superior to other element-doped GDY. In summary, beryllium-doped GDY has great potential as an outstanding anode material for lithium-ion batteries.