Precise determination of the structure‐property relationship of zeolite‐based metal catalysts is critical for the development toward practical applications. However, the scarcity of real‐space imaging of zeolite‐based low‐atomic‐number (LAN) metal materials due to the electron‐beam sensitivity of zeolites has led to continuous debates regarding the exact LAN metal configurations. Here, a low‐damage high‐angle annular dark‐field scanning transmission electron microscopy (HAADF‐STEM) imaging technique is employed for direct visualization and determination of LAN metal (Cu) species in ZSM‐5 zeolite frameworks. The structures of the Cu species are revealed based on the microscopy evidence and also proved by the complementary spectroscopy results. The correlation between the characteristic Cu size in Cu/ZSM‐5 catalysts and their direct oxidation of methane to methanol reaction properties is unveiled. As a result, the mono‐Cu species stably anchored by Al pairs inside the zeolite channels are identified as the key structure for higher C1 oxygenates yield and methanol selectivity for direct oxidation of methane. Meanwhile, the local topological flexibility of the rigid zeolite frameworks induced by the Cu agglomeration in the channels is also revealed. This work exemplifies the combination of microscopy imaging and spectroscopy characterization serves as a complete arsenal for revealing structure‐property relationships of the supported metal‐zeolite catalysts. A low‐damage HAADF‐STEM imaging technique is employed for direct visualization and determination of Cu species in ZSM‐5 zeolite frameworks. The structure of the Cu species are revealed based on the microscopy evidence and also proved by the complementary spectroscopy results. The mono‐Cu species stably anchored by Al pairs inside the zeolite channels are identified as the key structure for higher C1 oxygenates yield and methanol selectivity for direct oxidation of methane.