The changing hierarchical structure of the applied heterogeneous Cu/ZnO/Al2O3 material during methanol synthesis reactions hinders an efficient engineered process condition optimization, causing sub-optimal functional performance. A robust literature comparison is conducted to determine that activity is tightly coupled with Cu–Zn interactions. In order to investigate this physical behaviour further, characteristic experimental data is acquired through the catalytic reactor tests with an activated commercial catalyst, aged at different input measurements, monitored and characterized by the Brunauer–Emmett–Teller (BET), X-ray diffraction (XRD), scanning transmission electron microscopy (STEM) with energy dispersive X-ray spectroscopy (EDS), X-ray photoelectron spectroscopy (XPS), H2 transient adsorption (TA) and N2O pulsed surface oxidation (PSO) methodologies. It is shown that apparent rate law, exponents and activation energies do not vary significantly by increasing the ZnOX coverage from 7% to 23 %, while not all of ZnOX over-layer is catalytically active. For Cu/ZnO/Al2O3 with ZnOX over 7%, a highly-dispersed Al2O3 decreases the measured intrinsic kinetics of the Cu–Zn site, implying a steric hindrance effect. Finally, building on unveiled chemical relations, a thorough multisite system micro-kinetic model, based on systematic contribution analysis, mechanisms and quantitative density functional theory (DFT) constants is developed. Values were optimized using the sequential screening results for an industrially relevant application (the temperatures of 160–260 °C, 50 bar pressure, 12,000–200,000 h–1 gas hourly space velocity (GHSV) flow and relative feed compositions).Designed mathematical relationships can therefore be utilised to accurately predict the turnover, selectivity and stability/deactivation in correspondence to ZnOX over Cu.