Comprehensive first-principles calculations are performed to investigate the effects of the Silicon clusters (Si-CLs) anchored in nitrogen-doped defective graphene hybrid materials on their potential applications as very promising interface energy storing materials in lithium-ion batteries (LIBs). Three different kinds of defective models, graphitic, pyridinic, and pyrrolic graphene have been introduced in our work. First, the stability of Si-CLs deposited on various N-doped graphene (N-G) sheets has been investigated, and their electronic properties have been explored using first-principles theory. Second, single and multiple lithium (Li) atoms adsorption on Si-CLs anchored in N-G have been carried out to test the Li storage performances of the hybrids. Our results confirm that the N-doped pyridinic graphene hybrid is the most suitable materials for Li adsorption among those three different structural graphene sheets. Due to the symmetric vacancy presence, the binding strength of Si-CLs on N-doped defective graphene (N-DG) is much more powerful than that of graphitic one. Furthermore, the Li uptaking ability of Si/graphene (Si-G) is studied by calculating the binding energy of Li atoms. As a result, that N-G not only can be used as a bumper material restricting Si volume expansion, but can also provide extra intercalation places for Li atoms.