Terrestrial ecosystem is characterized by the transfer of most primary production to soil without much grazing by consumers and the persistence of organic matter (OM) in soil despite the abundance of heterotrophic microbes. Soil OM plays essential role in the formation of soil aggregate structure, microbial habitat, and water-holding and chemical-buffering capacities, providing physical and biochemical stability to the ecosystem. Textbook knowledge that soil OM persistence results from the large molecular size and recalcitrance of macromolecules such as lignin and humus may no longer be valid in light of the recent recognition that (i) most of OM in soil are microbial products that are relatively small in size and potentially labile (unstable), and (ii) the interaction of OM with soil mineral components strongly controls OM persistence. Here we present the results from our attempts to better understanding the OM-mineral interactions by soil physical fractionation techniques coupled with isotope and spectroscopic techniques. We will also discuss the role of geochemical processes in the soil OM persistence and those implications for ecosystem functioning.