In the study of mononuclear transition metal single molecule magnets (SMMs), extensive research has concentrated on identifying optimal coordination geometries around the central metal ion to enhance SMM properties. However, the role of non-covalent interactions in the second coordination sphere has been relatively underexplored. Here, we study the impact of non-covalent Cl⋯H interactions on the magnetic anisotropy of the central Co(II) ion in the distorted axially compressed octahedral complex CoCl2(tu)4 (1) (tu = SC(NH2)2). By performing cantilever torque magnetometry on 1, the orientation of the magnetic easy axis is found to deviate by almost 40° from the axial Co-Cl bond. Theoretical modelling on structural modifications of the structure of 1, quantifies how the distance between the Cl ligand and the nearest H-atom significantly influences the orientation of the magnetic easy axis and the D-value. Experimental chemical bonding analysis based on multipole modelling of synchrotron X-ray diffraction data on 1 reveal that the nearby H-atoms polarize the electron density of the Cl-ligands. This polarization results in reduced electron density at the axial positions on the Co octahedra, explaining the calculated increase in the magnitude of the D-value, when the H-atoms are moved away from Cl in silico. Topological analysis of theoretical electron densities on modified structures of 1 corroborates an increase in the electron density at the Co-Cl bond critical point, as the nearby H-atoms are moved further from Cl. These findings demonstrate the significant influence that non-covalent interactions have on the magnetic anisotropy of mononuclear transition metals and opens the possibility of utilizing these interactions in the design of transition metal based SMMs.