<p>Catalysts are core elements in the fields of modern chemical industry, energy conversion, and environmental protection. The precise regulation of their performance is crucial for achieving efficient, low-consumption, and sustainable chemical processes. With the rapid development of characterization techniques, especially real space transmission electron microscopy, catalytic research is undergoing a transformation from mean field analysis to the elucidation of local atomic-level structure-property relationships. This review focuses on the structure-property relationships of catalysts in real space and systematically reviews the core role of transmission electron microscopy techniques in revealing the intrinsic properties of catalysts across multiple scales. Starting from the regulation of potential functions of isolated atoms, the review discusses the effects of element selection, dual-atom synergy, heteroatom doping, and interface electric fields on the electronic structure and catalytic activity of single-atom catalysts. Subsequently, it conducts an in-depth analysis of the performance optimization mechanisms and characterization strategies caused by the symmetry breaking of degrees of freedom including lattice, charge, orbital, and spin as atoms aggregate to form nanoclusters and nanoparticles. Finally, the review prospects the complex correlations between the multi-scale dynamic structural evolution of catalysts and macroscopic performance in <i>in-situ</i> thermal, gas-phase, and liquid-phase catalytic environments, and emphasizes the key progress of a <i>in-situ</i> electron microscopy in capturing the dynamic behavior of catalysts in real reaction scenarios. This review aims to provide real space insights and envision the future direction of coupling the real space features of electronic structures and active sites with momentum space features of density of states and <i>d</i>-band theory for accurate prediction and rational design of high-performance catalysts.</p>