The in-situ direct imaging method (or in-situ atomic force microscopy) was used in studying interfacial reaction of biotite with low molecular weight organic acid. The low molecular weight organic acid used in the research is citric acid, which is one of the most important components of root exudate and, therefore, ubiquitous in the soil-plant system. Biotite, belonging in the mica group, is a kind of phyllosilicate mineral, which contains potassium (K), magnesium (Mg) and iron (Fe), essential for the crop growth. In order to observe how biotite is dissolved and changed in morphology changes in soil, an experiment was carried out with two pH treatments (4.0 and 6.0). Observation on the near-molecular scale reveals that biotite is a typical unit of layered structure, about 1 nm in height. The surface of biotite (001) is not smooth but full of terraces, debris and etches pits, which would disturb the dissolution process of biotite. In citric acid solution, 6.0 in pH, the terraces on the biotite (001) surface were dissolved at a constant rate of 0.01 μm²min^-1 within the first 45 min, and afterward, at a declining rate, and the original etch pits on the surface did not change much in area, but had edges blurred. Meanwhile, no new etch pits formed on the (001) surface. When treated with citric acid solution 4.0 in pH for 89 min, the biotite had a large number of irregular shaped tiny etch pits formed, which were randomly distributed on the (001) surface and mostly, about 0.7 ~ 1.1 nm in depth, and in addition quite a number of mini pits were forming and expanding into large ones. The original terrace on (001) surface also did not dissolve notably in area compared to that of the beginning situation. It is learnt from understanding of the theory of interactions on water-mineral interface that in weak acid environment, dissolution of biotite starts from defect/kink sites on the surface, one layer by one layer, and develops along the [hk0] direction, while releasing K from between layers and Si, Al, Mg and Fe from crystal lattices. ,To study dissolution of minerals under normal pressure and temperature, macroscopic researches usually require a long response time and a high dose of acid (e.g., strong acidity and high concentration), which may lead to deviation from the characteristics of minerals reaction under real conditions; on the other hand, the reaction process could not be visualized and the results need to be fit and explained with the help of other models and theories , which would usually make it more difficult to get results and the results more uncertain. But, the in-situ atomic force microscopy technology can overcome the shortcomings of the macroscopic method and realize real-time characterization of the reaction in the interface between phyllosilicate minerals and water through visualization, and hence validate macro research. Moreover, this technology may also provide information of high reference value to interfacial reaction in other fields.