It is well known that the performance of some key catalytic reactions has a strong dependence on metal catalyst surfaces. In the current work, this concept is further extended to the CuPd alloy-supported zirconium oxide inverse catalyst for CO2 hydrogenation to methanol. A combined DFT and microkinetic simulation study reveal that both the metal substrate surface and the precise exposed Cu or Pd metal atoms on the substrate have a pivotal influence on the catalytic mechanism and performance of the inverse catalyst for CO2 hydrogenation to methanol. Herein, CuPd(100), (111), and (110) surfaces with either Cu and Pd terminations have been examined, which provided five metal substrates as support for the inverse catalyst. Three different mechanisms, including the formate pathway, RWGS + CO-hydro pathway, and CO2 direct activation pathway, are explored under the same conditions; they take place at the interfacial sites between the metal alloy and oxide. The calculations indicated that the inverse catalyst with the CuPd(100) substrate demonstrates better performance than those with CuPd(110) and (111) for both formate and RWGS + CO-hydro mechanisms. Conversely, the reaction pathway is more sensitive to exposed atoms on the metal substrate. The best inverse catalyst, Zr3O6/CuPd(100) with either Cu or Pd terminations, demonstrated a methanol formation TOF above 0.30 site-1 s-1 and the selectivity was above 90% at 573 K, as evaluated from microkinetic simulation. The coverage analysis indicates the most populated species is HCOO*, which is consistent with experimental reports. Both kinetic and thermodynamics control steps are identified from DRC analysis for the best performing catalysts. Overall, the current study confirms the catalytic performance of the inverse Zr3O6/CuPd catalyst and demonstrates the tunable effects of the metal alloy substrate, which can facilitate effective optimization.