The new chain structures of the main o-LiB13C2 crystal with (C-B-C) chain are proposed to obtain new structures. The structural, mechanical, electronic, and dynamic properties of the newly designed structures with the B12(X-Y-X) and B12(X-X) (X and Y = B, C, and N) formulae are investigated by the first principles of density functional theory (DFT), and detailed comparisons with the main crystal between the stable and unstable structures are given. It is found that the structures with (N-C-N), (C-Va-C), and (N-Va-N) chains meet the thermodynamic, mechanical, and dynamic stability conditions. The tensile strengths of the stable structures are examined, and it is observed that the (N-C-N) chain system underwent a phase change and turned into a new stable structure that has an (N-Li-N) chain and different bonding geometry and characteristics in interstitial space between the B12 icosahedra. A detailed geometry analysis utilizing the selected bond lengths, volume and surface area of B12 icosahedron is offered. The partial density of states, charge and critical point analysis, electron density differences are presented to clarify the bonding situations of the structures. The Bader charges of B12 icosahedra in the stable structures have positive, in contrast to Wade’s rule. The existence of the chain in the B12(X-Y-X) and B12(X-X) compounds affects the charging behavior of B12 icosahedron due to the different asymmetrical charge densities. The mechanical properties and their anisotropies are calculated for different lattice directions and visualized through 2D and 3D graphs. Based on the actual bonding characteristics, the bond resistance model with Phillips ionicity and Mulliken bond overlap populations, the bond electronegativity model, and the bond valence model, the hardnesses of the stable structures are calculated by each model. It is found that the stable structures have hardnesses spanning a wide range of 8–35 GPa due to the different models. The origin and dynamic instability of the unstable structures are examined. It is concluded that the existence of Li atoms and different chains, which include the different electronegativity of atoms within the structure, have essential roles in charge transfers, chain geometries, vibrational behavior, and then the stability of the structures.