There are lots of new growths in red clay presenting dark brown color and regular or irregular shapes in southern China. Because of high Fe and Mn concentrations, these nodules are called iron-manganese nodules. As a product of soil temperature, moisture and redox conditions, these iron-manganese nodules, especially the circular bands in the inner nodules, were considered as a kind of environmental information carrier, and aroused widespread interest of researchers. Therefore, the study of the tiny area inside the nodules helps to understand the weathering process of the parent material and the formation process of the nodule. In this paper, using a microbeam X-Ray fluorescence spectrometer, tiny areas of inner iron-manganese nodules collected from Quaternary red earth were analyzed. The results show that the microbeam X-Ray fluorescence spectrometer can be used to analyze tiny areas of inner nodules with higher accuracy. Microscopic images of the nodule show three dark bands and two light bands alternating from the core to the edge. The X-ray fluorescence spectrum analysis indicates that the dark bands contained more Mn and less Si and Al than light bands. Combined with previous research, the dark bands represent periods of drought, and light bands represent humid periods.