For a long time, quite a number of people one-sidedly believe that soil science is merely an applied science, and its research tools are merely experimental, while its research methodology should be holistic and integrative. In this paper, systems analysis was done of the perniciousness of this one-sided presumption to development of the soil science, and it was proposed that development of the soil science in future should stress the use of analytical methods and a natural systematic integration should be realized on the basis of such in-depth analyses. Three basic viewpoints were then put forward and elaborated: 1) it is essential to be fully aware that the peculiarities of the soil systems root in their fundamental impacts on subatomic structures. For example, in common aqueous solutions, Li , K and Cs will definitely not exceed 1.00 in effective charge and instead should fall below 1.00 due to cationic volumes and hydration effects; however, their effective charges burgeon respectively to 1.05, 1.94 and 2.40 when these ions are placed at the interface of clays in aqueous solutions, as a result of the profound impact of clay on the energetic and quantum states of these cation electrons. In other words, cations (as well as atoms and molecules) at clay interfaces are essentially different from those in aqueous solutions. 2) Considering peculiarities of the soil systems, methodologically the soils should be hierarchized by scale i.e. macroscopic, mesoscopic, molecular, atomic and subatomic scales, and eventually analyzed by means of the principles and methodology of quantum mechanics at the subatomic scale. And 3) Through researches based on the quantum effect unique to the soil, direct correlations between subatomic structures, soil microscopic mechanisms and macroeffect could be established, hence to realize, an natural conversion of scientific principles between different scales of soil. And in the end an independent and self-consistent pedological knowledge system will be constituted. Here it is a must to emphasize that this paper is intended to provide some ideas about methodology of the research on basic soil science. Although it may be too much of a generalization for our arguments to be just supported by several special examples, the particularities of the soil systems those samples reflect sufficiently express the necessity to establish an independent and self-consistent knowledge system for soil science, and the importance of analytical methods in the establishment.