Endohedral group14-based clusters with the encapsulation of a transition metal, which are termed [TM@Em]n- (TM = transition metal and E = group-14 elements), have lots of potential applications and have been used as interesting building blocks in materials science. Nevertheless, their electronic structures and stability mechanism remain unclear. In this paper, we systematically study the geometries, electronic structures, and bonding properties of [TM@E9]n- clusters which are the smallest endohedral group-14-based clusters synthesized so far, by using density functional theory (DFT) calculations. The calculation results reveal the important role of TMs in affecting the structures and bonding interactions in the [TM@E9]n- cluster. In the presence of a TM, the cluster geometry could change from a monocapped square antiprism (C4v) for empty [E9]4- cages to a tricapped trigonal prismatic geometry (D3h) for [TM@E9]n-. By using the energy decomposition analysis (EDA) method, the bonding properties between the endohedral TM and E9 cluster have been thoroughly investigated. It was found that the origin of stability of these clusters is from the large electrostatic attraction with significantly reduced Pauli repulsion. In the case of orbital interactions, the π back-donations from d orbitals of the TM to the cluster make important contributions. More interestingly, the 1D-chain and 2D-sheet nanostructures based on the [Ni@E9] cluster have been theoretically predicted. The band structure and density of states analysis revealed that all of these nanostructures are metallic and their excellent thermodynamic stability has been confirmed by using ab initio molecular dynamics (AIMD) simulations.