The chemistry of Al transformation has been well documented, though little is known about the mechanisms of structural perturbation of Al precipitates by carbonates at a molecular level. The purpose of the present study was to investigate the structural perturbation of Al precipitates formed under the influence of carbonates. Initial carbonate/Al molar ratios (MRs) used were 0, 0.1, and 0.5 after aging for 32 days, then the samples were analyzed by X-ray absorption near edge structure spectroscopy (XANES), X-ray diffraction (XRD), Fourier-transform infrared absorption spectroscopy (FTIR), and chemical analysis. The XRD data were in accord with the FTIR results, which revealed that as the carbonate/Al MR was increased from 0 to 0.1, carbonate preferentially retarded the formation of gibbsite and had relatively little effect on the formation of bayerite. As the carbonate/Al MR was increased to 0.5, however, the crystallization of both gibbsite and bayerite was completely inhibited. The impact of carbonate on the nature of Al precipitates was also evident in the increase of adsorbed water and inorganic C contents with increasing carbonate/Al MR. The Al K- and L- edge XANES data provide the first evidence illustrating the change in the coordination number of Al from 6-fold to mixed 6- and 4-fold coordination in the structural network of short-range ordered (SRO) Al precipitates formed under the increasing perturbation of carbonate. The fluorescence yield spectra of the O K-edge show that the intensity of the peak at 534.5 eV assigned to σ* transitions of Al–O and O–H bonding decreased with increasing carbonate/Al MR. The XANES data, along with the evidence from XRD, FTIR, and chemical analysis showed clearly that carbonate caused the alteration of the coordination nature of the Al–O bonding through perturbation of the atomic bonding and structural configuration of Al hydroxides by complexation with Al in the SRO network of Al precipitates. The surface reactivity of an Al–O bond is related to its covalency and coordination geometry. The present findings were, therefore, of fundamental significance in understanding the low-temperature geochemistry of Al and its impacts on the transformation, transport, and fate of nutrients and pollutants in the ecosystem.