In this review, the evolution of Soil Organic Matter (SOM) research was traced back to outline the main achievement of understanding SOM in relation to its ecological functioning, particularly of carbon sequestration against climate change. The short-coming of soil humus theory, knowledge of SOM protection and stabilization, framework of newly emerged Humeomics as well as the increasingly active study of molecular organics in soils were analyzed and discussed, highlighting the importance of re-visiting SOM in term of structure-property-functions for the main mission of modern soil science. There were limitations of soil forming conditions, fraction separation procedure and single molecule identification for understanding the huge complex humus of larger sized synthesized molecules. Thanks to the ever-active studies of soil (organic) carbon sequestration and stabilization focusing on the association status of SOM with soil components, SOM has been increasingly recognized as an assemblage of metabolites from life activities on or in soil, with different allocation or protected in mineral/organic complex phases, which could be traced by biomarker molecules. Using such biomarker molecules as a target (like primer in molecular microbiology), all the molecules of SOM could be digested and isolated for qualitative or quantitative identification with GC/MS high resolution technologies. Such development has emerged a new paradigm of molecular SOM study, finally as SOMics as a modern soil science frontier. The functioning of SOM for stabilizing soil structure, enhancing reactivity and promoting biological resistance could be correlated to the paradigm of abundance, composition, structure and functions rather than the content and recalcitrance of SOM. This may deserve urgent studies to quantify and parameterize the defined paradigm based on the molecular composition of SOM. Again, such theory and technology development could provide a tool to manage SOM in term of carbon sequestration but revalorizing bioactivity in ecosystems, especially in agroecosystems. We believe such studies could rather depict the nature of SOM and of soil in relation to its ecological services and functioning, which will be the focus of soil science in serving the sustainable development of human society.