The atomic-scale surface fractal, which can notably affect gas adsorption, is a prominent form of geometric heterogeneity at the surfaces of the pore structure of shale. Systematically evaluating the effect of the atomic-scale surface fractal on gas adsorption remains an open research question. In this study, we investigated the single-component adsorption of methane, nitrogen, and carbon dioxide in fractal shale nanopores at 298 K by Monte Carlo simulations in the grand canonical ensemble. We carved out the atomistic nanopore models by fractal surfaces created using the diamond-square algorithm with the surface fractal dimension ranging from 2 to 2.9. We evaluated the variation in the adsorption energy, the absolute and excess adsorbed density, and the adsorption layer density with the surface fractal dimension, which indicates that the atomic-scale surface fractal is an unfavorable factor for the single-component adsorption of methane, nitrogen, and carbon dioxide. The findings may enhance our understanding of the mechanism for heterogeneous gas adsorption in shale.