Selenium (Se) is an essential element for the human body. Humans meet their basic Se requirements primarily through food consumption. The largest Se-rich contiguous area in China is located in the southeast of Guangxi. In this study, the Se accumulation and translocation in the Guangxi rice–soil system was assessed. Organically bound Se (O-Se) was found to be the main type of soil Se (72.5%), and had a good linear relationship with soil total Se (TSe) and soil organic matter (SOM); the three forms were closely related and thus, affected each other. The contents of Se in the various plant organs were highly correlated. The roots had the greatest Se concentration, followed by the stems, grains, and lastly the leaves. The distribution coefficient of grain/stem (0.74) was greater than that of grain/leaf (0.54), suggesting that the migration of Se in plants may have apical dominance and/or reproductive advantages. Ligand-exchangeable Se, water-soluble Se, and residual Se had little effect on the accumulation of Se in the soil and plants. The soil S content showed no significant correlation with the various types of soil Se and TSe, but showed a low correlation with the Se content in various plant organs. SOM played a special role in the translocation of Se between the soil and plants, which affected the absorption and accumulation of Se by plants. SOM can affect the content of O-Se and, consequently, of TSe in the soil. SOM can also directly or indirectly affect the Se content in various plant organs, especially the Se concentration in rice grains.