Recently, single-atom catalysts (SACs) have attracted significant attention because of their efficient utilization of precious metals and unique properties. However, the rational design of improved SACs faces tremendous challenges, largely as a result of elusive active sites and complex reaction mechanisms under operating conditions. Herein, by combining density functional theory (DFT) calculations and uncertainty analysis with microkinetic modeling (MKM), we elucidated the local configurations and CO oxidation mechanisms of Ir1/TiO2 catalysts under operating conditions. Our findings reveal that Ir1/TiO2 catalysts do not have static site configurations or CO oxidation mechanisms; instead, they dynamically adapt their site structures, kinetically relevant steps, and reaction pathways in response to varying conditions. However, largely as a result of intrinsic uncertainties of DFT energetics, kinetic modeling is limited in fully capturing detailed reaction kinetics. Nevertheless, this study sheds light on the complexity of SACs, which is crucial for the rational design of improved site motifs for targeted chemistry.