This work concerns the special conformational behaviors for di‐substituted cyclohexanes that inherently depend on spatial orientations of side chains in flexible cyclic ring. The 1,3‐dimethylcyclohexane and 1,4‐dimethylcyclohexane in both cis‐ and trans‐configurations were focused here to unravel their inversion‐topomerization mechanisms. Full geometry optimizations were separately performed at B3LYP/6‐311++G(d,p) and MP2/6‐311++G(d,p) levels to explicitly identify all distinguishable molecular structures, and thereby the complete interconversion routes were carefully explored. Additional quantum calculations were carried out by G4 and CCSD(T)/6‐311++G(d,p) methods to acquire high‐level single point energies. With respect to quantum results, conformational analysis was conducted to study determinations, thermodynamic stabilities, and relative energies of distinct conformers. Temperature‐dependent populations of local minima for each dimethylcyclohexane were computed by Boltzmann distribution within 300–2500 K. Moreover, their unique inversion and topomerization processes were fully investigated, and potential energy surfaces were illustrated with the rigorous descriptions in two or three‐dimensional schemes for clarify.