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Atomic-scale defects in two-dimensional transition metal dichalcogenides (TMDs) often dominate their physical and chemical properties. Introducing defects in a controllable manner can tailor properties of TMDs. For example, chalcogen atom defects in TMDs were reported to trigger phase transition, induce ferromagnetism, and drive superconductivity. However, reported strategies to induce chalcogen atom defects including postgrowth annealing, laser irradiation, or plasma usually require high temperature (such as 500 °C) or cause unwanted structural damage. Here, we demonstrate low-temperature (60 °C) partial surface oxidation in 2D PdSe₂ with low disorder and good stability. The combination of scanning tunneling microscopy, X-ray photoelectron spectroscopy, and density functional theory calculations provide evidence of atomic-scale partial oxidation with both atomic resolution and chemical sensitivity …