Abstract: Background Metal oxides are important active components and cementing agents in soils.Methods In this study, representative soils including Black soil, Cinnamon soil, Red soil, and Latosol were selected. A combination of wet sieving and chemical selective extraction was employed to analyze the variations in the contents of free, amorphous, and complex Fe, Al, and Mn oxides within water-stable aggregates of different size classes, as well as their controlling factors. Results 1) with decreasing aggregate size, the contents of free and complex Fe and Al oxides in Acrisol and Ferralsol, and those of amorphous Fe and Mn oxides in Chernozem, exhibited an increase followed by a decrease; the amorphous Al oxide content in Luvisol showed a decreasing–increasing trend; the amorphous Fe oxide content in Acrisol gradually decreased, while the contents of complex Fe and Al oxides in Chernozem progressively increased. 2) Free Fe and Al oxides varied most significantly with aggregate size in Fe–Al cemented soils, whereas amorphous oxides showed the greatest variations in organically cemented soils. 3) Free Fe and Mn oxides were mainly positively influenced by clay content (r = 0.74 and 0.69, p < 0.001), amorphous Fe oxide was mainly positively influenced by soil organic carbon (r = 0.79, p < 0.001), while other forms of metal oxides were predominantly negatively affected by pH (r < –0.49, p < 0.01). Conclusion These findings reveal the spatial differentiation of soil metal oxides at the aggregate scale and provide scientific insights into the mechanisms of aggregate formation and stabilization, as well as related soil processes.