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For soils and sediments, which are complex and heterogeneous, root-triggered processes, bioturbation of benthic communities, and local decomposition of reactive organic materials can greatly increase their biogeochemical heterogeneity. In practice, common monitoring methods can only be used to determine the centimeter- to millimeter-scale heterogeneity from vertical or horizontal one-dimensional profiles. However, significant heterogeneity exists in both soils and sediments on the millimeter to sub-millimeter scales. Therefore, in-situ and high-resolution sampling and imaging methods are essential to capture the spatial and temporal heterogeneity of soils and sediments. This article reviews micro-scale sampling methods in soil and sediments, including diffusive equilibration in thin films (DET), diffusive gradient in thin films (DGT), planar optodes (PO), nanoparticle- and microparticle-based luminescence imaging, and soil zymography. Besides, we introduce their imaging principles and approaches in detail, and discuss some problems and solutions during imaging. Micro-scale sampling and imaging methods have given us many insights into the biogeochemical processes in soils and sediments, but the full potential of these methods has not been exhausted yet. Finally, the potential directions for the development of micro-scale sampling methods in the study of complex biogeochemical processes in heterogeneous soils and sediments are prospected. [ABSTRACT FROM AUTHOR]