Molecules confined in the nanoscale regions usually exhibit intriguing physical and chemical properties. The present paper reports on the direct observation of charge transfer behaviors in spatial confined xenon (Xe) atoms. Individual Xe atoms are trapped at 300 K in nano-cages consisting of silica hexagonal prisms forming a two-dimensional (2D) array on a planar surface. In-situ synchrotron-based ambient pressure X-ray photoelectron spectroscopy (AP-XPS) reveals that the charge transfer takes place at the Xe atoms which are extremely confined between the 2D framework and the Ru(0001) support, in which the interfacial distance can be controlled by the coverage of chemisorbed oxygen on Ru(0001). Density functional theory (DFT) calculations further corroborate these significant charge transfer interactions between the trapped Xe atoms and silica/Ru(0001) systems, opening exciting opportunities for the study of individual noble gas atoms in confinement.