Black rice has very superior medicinal value. Since ancient times, it has been used as a nourishing and health-care rice for medicine and food. It has powerful functions such as disease prevention, regulation of circadian rhythm, and promotion of physical recovery. It is suitable for long-term consumption. In this paper, optical microscope, scanning electron microscope and energy dispersive spectrometer (SEM-EDS) were used successively to visualize and quantitatively analyze the element distribution in the chalky and non-chalky areas of two indica rice varieties in Southern Henan. The results showed that black rice has rich C and O content, followed by N, P, S content, Mg, K, Ca, Mn, Zn content is less. The content of the O element in the chalky area is higher than that of the non-chalky area, while many elements such as C, N, P, S are significantly higher in the non-chalk areas than in the chalk areas; especially the N and S elements are the best indicators of protein, the content in chalkiness area was lower than that in non-chalky area. It can be inferred that the protein content in non-chalky part was higher than that in chalky part, that is, chalkiness character of black rice would affect the nutritional quality of rice. Therefore, our results showed the distribution of elements and protein in black rice, which is helpful for the cultivation of new high-quality black rice varieties in the future.