A new strategy of sodium ion batteries with the hybrid storage of Li and Na ions has attracted much attention in the field of large-scale energy storage. For revealing the mechanism of hybrid storage of Li and Na atoms in carbon materials, the lowest energy configuration, adsorption energy, differential charge density and density of states of LixNay clusters on graphene, as a structural unit of carbon materials, were calculated and investigated based on first principles density functional theory. The calculation results show that the deposition behavior of single Li or Na atoms on graphene is similar, and both are preferentially deposited at the hollow of graphene (H-site). The Li atom is deposited preferentially over the Na atom, and the deposition height of the Li atom is lower. When the total number of metal atoms x + y ≥ 3, LixNay clusters are deposited on graphene in the form of a stereotypical atomic cluster, in which the Li atom is usually at the bottom of the LixNay cluster, while the Na atom is usually at the top of the cluster. The electronic structure analysis shows that the electrons of the LixNay cluster are transferred to the anti-bonding π orbitals adjacent to graphene. The 2s orbitals of Li atoms and the 2s and 2p orbitals of Na atoms are hybridized with the 2p orbitals of C atoms. Therefore, the Li-C bonds or Na-C bonds formed between Li or Na atoms and C atoms of graphene are usually ionic bonds with partial covalent bond properties. Meanwhile, the Li-Li, Na-Na or Li-Na bonds formed inside LixNay clusters are usually multiple metal-metal bonds.