To enhance Se accumulation in rice and meet human nutritional needs of Se by daily diet, an experiment was conducted to study the kinetics of accumulation and distribution of Se in rice in a yellow muddy soil treated with nanoscale Se composite fertilizers. The results showed that the studied rice cultivar had a relatively low ability to accumulate Se from the yellow muddy soil, but the uses of Se fertilizers significantly increased Se accumulation in rice, and Se accumulation in rice tissues positively correlated with the Se fertilization rate. A large variation in Se concentration was observed in different rice tissues at different growth stages. The highest Se-bioconcentration was observed at the booting stage, and Se distribution in rice at the maturity stage was in an order of stem > leaf > rice grain > root > husk. Se flow was figured out during rice growth cycle as follows: Se firstly accumulated in leaves from roots and stems at tillering stage, then flowed from leaves to stem at booting stage, moving up from roots to leaves and panicle by stem at grain-filling stage, and finally stored in rice panicle from leaves at maturity stage. The present study will be helpful for Se biofortification on rice.