Light-induced oxidative damage of DNA by 1O2 generated from photoexcited C60 was observed at the single-molecule level by atomic force microscopy (AFM) imaging. Two types of DNA origami with uniform morphologies were immobilized on a mica surface and used as DNA substrates. Upon visible light irradiation (528 nm) in the presence of a C60 aqueous solution, the morphology changes of DNA origami substrates were observed by time-lapse AFM imaging at the single-molecule level by tracking a discrete DNA molecule. The origami showed nicked and flattened morphologies with relaxed features caused by the covalent cleavage of the DNA strands. The involvement of 1O2 in the on-surface DNA damage was clearly confirmed by AFM experiments in the presence of a 1O2 quencher and ESR measurements with a spin-trapping agent for 1O2. This study is the first example of single-molecule observation of oxidative damage of DNA by AFM with corresponding morphology changes in a photocontrolled and time-dependent manner by 1O2 generated catalytically from photoexcited C60.