Soil selenium (Se) sequestration and transformation, which are strongly controlled by soil redox conditions, are critical for understanding the mobility and bioavailability in the environment. Thus, the effect of redox potential on Se transformation was investigated for exploring the release mechanism of Se in soil. Soils were incubated under anoxic condition in four treatments at room temperature over 56 days, and the soil solution pH, Eh, and Fe and Se concentrations were measured at given reaction time. The sequential extraction and X-ray photoelectron spectroscopy (XPS) were used to obtain the species distribution of Se in soil. High-resolution transmission electron microscopy (HR-TEM) was employed to observe morphology characteristic of soil. Parts of soil Se can be released into solution, and Se speciation in soil changed during the incubation period. XPS and sequential extraction analyses revealed that the primary speciation of Se in soil was elemental Se, and metallic selenides were formed under aerobic condition. Moreover, XPS and HR-TEM data revealed the crystalline state of iron oxides in soil changed after anoxic incubation, and certain amorphous iron oxides were formed. Se release is activated by short-term incubation, whereas Se can be transformed into less soluble state after long-term incubation. Organic matter takes extremely an important role in Fe oxide reductive dissolution and Se transformation. This study is useful to understand the environmental behaviors of Se and enhance the application of Se fertilizers effectively and safely in Se deficiency area.