Structures exert significant controls on hydrothermal mineralization, although such controls commonly have cryptic expression in geological datasets dominated by 2D maps. Analysis of spatial patterns of mineral deposits and quantification of their correlation with detailed structural features are beneficial to understand the plausible structural controls on mineralization. In this paper, a series of GIS-based spatial methods, including fractal, Fry, distance distribution and weights-of-evidence analyses, were employed to reveal structural controls on copper mineralization in the Tongling ore district, eastern China. The results indicate that Yanshanian intrusions exert the most significant control on copper mineralization, followed by EW-trending faults, intersections of basement faults and folds. The scale-variable distribution patterns of copper occurrences are attributed to the different structural controls operating in the basement and sedimentary cover. In the basement, EW-trending faults serve as pathways for channeling Yanshanian magma from a deep magma chamber to structurally controlled trap zones in the caprocks, imposing an important regional control on the spatial distribution of Cretaceous magmatic-hydrothermal system genetically related to copper mineralization. In the sedimentary cover, bedding-parallel shear zones, formed during the progressive folding and shearing in Indosinian and overprinted by tensional deformation in Yanshanian, act as favorable sites for hosting, focusing and depositing the ore-bearing fluids, playing a vital role in the localization of stratabound deposits at fine scale.