During flood irrigation, the physical and chemical properties of the soil change to some extent, and then alter the content and fraction of soil Se. At present, soil properties and the process of Se migration and transformation during flood irrigation are not fully understood. This study used indoor simulation experiments to analyze the variation of the soil Se fraction with time and its relationship with the variations in soil physical and chemical properties during flooding. It also explored the migration characteristics of Se in soil during irrigation, and proposed suggestions for the development of Se-rich agriculture. The results showed that residual Se, humic acid-bound Se, and strongly organic-bound Se were the main fractions of soil Se, accounting for, on average 35.3%, 20.3%, and 27.6% of the total Se. Flood irrigation could accelerate the loss of Se in soil, decrease the bioavailability of soil Se, and the content of water-soluble and ion-exchangeable Se decreased from nearly 8.0% to 5.0% of total Se. As such, it is necessary to rationally develop and utilize Se-rich land resources to ensure the sustainable development of healthy agricultural production.