The development of an efficient catalyst especially with a high productivity for decarboxylation of L-lysine to cadaverine, is of both industrial and economic significance. Here, we reported the synthesis of RuO2 well-confined in the supercage of FAU zeolite (RuO2@FAU) through in situ hydrothermal strategies. A set of characterizations, such as XRD, Raman, TEM, XPS, NH3-TPD and N2 physical adsorption, confirmed the successful encapsulation of RuO2 clusters (~1.5 nm) inside the FAU zeolite. RuO2@FAU had the higher cadaverine productivity of 120.9 g/L/h/mmol cat., which was almost six times that of traditionally supported ruthenium oxide catalysts (21.2 g/L/h/mmol cat.). RuO2@FAU catalysts with different ammonia exchange degrees, as well as different Si/Al ratios were further evaluated. After optimization, the highest cadaverine productivity of 480.3 g/L/h/mmol cat. was obtained. Deep analysis of the electronic properties of RuO2@FAU indicated that the surface defect structures, such as oxygen vacancies, played a vital role in the adsorption or activation of L-lysine which finally led to a boosted performance. Furthermore, the mechanism of decarboxylation of L-lysine to cadaverine was proposed.