The dynamic structural evolution of Rh species in mordenite (MOR) zeolite was investigated using in situ spectroscopic techniques and DFT calculations. In situ X-ray absorption spectroscopy and operando infrared (IR) revealed that metallic Rh species were oxidized to afford isolated [Rh(NO)2]+ species under NO flow at 200°C, whereas small Rh metal clusters is formed under the subsequent H2 flow. Ab initio thermodynamics analysis shows that the plausible structures under NO and H2 at 200°C are [Rh(NO)2]+ and Rh clusters in MOR, which is consistent with the experimental observations. A comparative study of Rh-loaded Al2O3 suggests that Al sites in MOR increase the thermodynamic stability of isolated Rh+ species and thus prevent their overoxidation to Rh2O3 under NO. NO capture in the form of [Rh(NO)2]+ and its selective reduction toward NH3 under H2 flow were observed by in situ IR measurements. The RhMOR catalyst exhibited ~60% of NOx conversion above 200°C under periodic lean/rich conditions. Transition state calculations showed that the activation barrier for NO reduction to NH3 on [Rh(NO)2]+ (178 kJ/mol) is higher than that for Rh13 (156 kJ/mol), suggesting that Rh metal clusters are preferable NH3 formation sites, where the Rh13-catalyzed NO reduction into N2 and N2O was less preferable than NH3 formation, which is consistent with the experimental results. Combined with operando IR experiments under lean (NO + O2) and rich (NO + H2) conditions, we show that the reversible dynamic structural evolution of Rh species ([Rh(NO)2]+ Rh metal clusters under lean and rich conditions) is a key mechanistic feature for unsteady-state de-NOx via the capture of NO, its selective reduction to NH3, and the selective reduction of NO with NH3 formed in situ.