We propose an effective deep learning model to denoise scanning transmission electron microscopy (STEM) image series, named Noise2Atom, to map images from a source domain [Formula: see text] to a target domain [Formula: see text], where [Formula: see text] is for our noisy experimental dataset, and [Formula: see text] is for the desired clear atomic images. Noise2Atom uses two external networks to apply additional constraints from the domain knowledge. This model requires no signal prior, no noise model estimation, and no paired training images. The only assumption is that the inputs are acquired with identical experimental configurations. To evaluate the restoration performance of our model, as it is impossible to obtain ground truth for our experimental dataset, we propose consecutive structural similarity (CSS) for image quality assessment, based on the fact that the structures remain much the same as the previous frame(s) within small scan intervals. We demonstrate the superiority of our model by providing evaluation in terms of CSS and visual quality on different experimental datasets.