Gardner, a famous soil physicist, believes that the current soil science knowledge is too fragmented, it is therefore necessary to build a systematic soil science knowledge system. Churchman, an Australian scholar, pointed out that the new knowledge system of soil science must break the boundaries of each soil science branch. In this paper, the necessity as well as the theoretical and methodological basis of the reconstruction of the core knowledge system of soil science were systematically analyzed. This paper indicates that the quantum mechanical description of soil electric-atom interaction can be the theoretical basis for building core knowledge systems of basic soil science, and the quantitative description of the five macro physical quantities, including electrostatic force, long-range van der Waals force, osmotic force, hydrophilic and hydrophobic force, can break the boundaries of each soil science branch, and then study soil as a whole. Based on the quantum mechanics of soil electric-atom interaction and with the help of five macroscopic physical quantities, the systematic description of soil matrix process, interface process and pore process can be realized. Since the physical, chemical and biological processes in soil can be reduced to the correlation and coupling of soil "matrix processes", "interface processes" and "pore processes" at different scales, it is expected to build a new core knowledge system of basic soil science based on the theory and method proposed in this paper.