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Core IdeasThe spatial arrangements of soil MOAs are highly heterogeneous.The processes of carbon binding in different soil types are different.Combination of SR‐FTIR mapping and 2DCOS could in situ characterize the sequences of MOAs. Direct characterization of spatial distribution and binding environments of soil mineral‐organic associations (MOAs) are imperative for understanding the mechanism of C storage. Here, we propose a new strategy of synchrotron‐radiation‐based Fourier transform‐infrared (SR‐FTIR) technology and two‐dimensional FTIR correlation spectroscopy (2DCOS) analysis to simultaneously characterize the MOAs extracted from two types of soil, which one is classiðed as Ferralic Cambisol and another is Typic Hapludoll. This study successfully showed the spatial heterogeneity by SR‐FTIR mapping, which illustrated that the different soil types had different spatial arrangements at the microscale scale. Moreover, the overlapped one‐dimensional (1D) SR‐FTIR spectra and various sequence orders in two types of soil were demonstrated by 2DCOS analysis. The results showed that the intra hydrogen bonds in clay‐OH minerals and Si‐O‐metal bonds were more highly reactive in the Ferralic Cambisol soils than that in the Typic Hapludoll soils, which was critical for understanding the binding processes in soil micro‐environments.