Two new transition metal complexes with 1-methylimidazole (1-MeIm) and azide as ligands, namely, [Co(1-MeIm)4(N3)2] (1) and [Ni(1-MeIm)4(N3)2] (2), have been synthesized and characterized by IR, Raman, UV-Vis and XPS spectroscopy. Their crystal structures were solved by single-crystal X-ray diffraction. The supramolecular self-assembly of the two complexes is governed by non-classical C-H⋯N hydrogen bonds and C-H⋯π interactions. Lattice energies and intermolecular interaction energies for various molecular pairs are quantified using the PIXEL method. DFT computational studies to assess the binding energy through modern tools like non-covalent interaction (NCI plots) analysis and reduced density gradient (RDG) analysis have also been carried out. A detailed analysis of geometric descriptors revealed the existence of quasi-isostructural pairs or 'main-part' isostructuralism in a series formed by 1, 2, and a related cadmium complex, being more evident in the 1/2 pair. DFT studies using theoretical models have been used to disclose the relative importance of the H-bond and C-H⋯π noncovalent interactions. Magnetic measurements for compound 1 show weak ferrimagnetic coupling between adjacent M(II) centers, mediated by H-bonding and C-H⋯π non-covalent interactions.