Cu-based catalysts have attracted much interest in CO2 hydrogenation to methanol because of their high activity. However, the effect of interface, coordination structure, particle size and other underlying factors existed in heterogeneous catalysts render to complex active sites on its surface, therefore it is difficult to study the real active sites for methanol synthesis. Here, we report a novel Cu-based catalyst with isolated Cu active sites (Cu1-O3 units) for highly selective hydrogenating CO2 to methanol at low temperature (100% selectivity for methanol at 180 oC). Experimental and theoretical results reveal that the single-atom Cu-Zr catalyst with Cu1-O3 units is only contributed to synthesize methanol at 180 oC, but the Cu clusters or nanoparticles with Cu-Cu or Cu-O-Cu active sites will promote the process of reverse water gas shift (RWGS) side reaction to form undesirable byproducts CO. Furthermore, the Cu1-O3 units with tetrahedral structure could gradually migrate to the catalyst surface for accelerating CO2 hydrogenation reaction during catalytic process. The high activity isolated Cu-based catalyst with legible structure will be helpful to understand the real active sites of Cu-based catalysts for methanol synthesis from CO2 hydrogenation, thereby guiding further design the Cu catalyst with high performance to meet the industrial demand, at the same time as extending the horizontal of single atom catalyst for application in the thermal catalytic process of CO2 hydrogenation.