Stacked two-dimensional (2D) materials as bulk materials are more practical to be anodes of Li-ion batteries than their monolayers due to the easier operation, while the ion kinetics and capacity are usually deteriorated by the geometric constraint in stacked structures. Herein, we perform first-principles calculations to explore anode performances of the stacked graphdiyne (GDY) where the functional group is intercalated to enlarge the interlayer distance. Compared to the monolayer GDY, which has a diffusion barrier of only 0.315 eV and capacity as high as LiC3, the pristine stacked GDY presents lower capacity (LiC6) and higher diffusion barrier (0.638–0.922 eV) due to the geometric constraint, while after functionalization, the stacked GDY exhibits excellent properties for storing ions similar to the monolayer GDY. A good electronic conductivity is also confirmed by the density of states. Our study indicates that functionalization is an effective pathway to improve the anode performances of stacked 2D materials by optimizing the interlayer structure.