Van der Waals heterostructures composed of different two-dimensional (2D) materials have attracted considerable attention as the anodes for lithium-ion batteries (LIBs), and doping can significantly affect their electronic structures and lithium diffusion barriers. Herein, the effects of heteroatom (X = N, O, P and S) doping in graphene of the graphene/silicene (G/Si) heterostructure are comprehensively investigated based on first-principles calculations. The stacking stability and mechanical stiffness of G/Si and doped G/Si (XG/Si) show that N-doping can increase the structural stability of G/Si, ensuring good cycling performance. The densities of states indicate that the dopant (N, O and S) can greatly improve the electronic conductivity of G/Si. Importantly, the adsorption and diffusion behaviors of Li are mainly affected by the dopant and the doping site, leading to the ultrafast Li diffusivity. Thus, N-doped G/Si at doping site 1 (S1) exhibits a good balanced property, which shows a good potential to improve the electrical performance of G/Si materials and can guide the selection of dopants in other 2D anode materials for LIBs.