MnCoGe-based materials have the potential to exhibit giant magnetocaloric effects due to the coupling between magnetic ordering and a martensitic phase transition. Such coupling can be realized by matching the temperatures of the magnetic and structural phase transitions. To understand the site preference of different elements and the effect of hole or electron doping on the stability of different polymorphs of MnCoGe, crystal orbital Hamilton population (COHP) analysis has been employed for the first time to evaluate peculiarities of chemical bonding in this material. The shortest Mn–Mn bond in the structure is found to be pivotal to the observed ferromagnetic behavior and structural stability of hexagonal MnCoGe. Based on this insight, eliminating antibonding features of the shortest Mn–Mn bond at the Fermi energy is proposed as a feasible way to stabilize the hexagonal polymorph, which is then realized experimentally by substitution of Zn for Ge. The hexagonal MnCoGe structure is stabilized due to depopulation of the antibonding states and strengthening of the Mn–Mn bonding. This change in chemical bonding leads to anisotropic evolution of lattice parameters. The structural and magnetic properties of Zn-doped MnCoGe have been elucidated by synchrotron X-ray diffraction and magnetic measurements, respectively.