The differences in natural selenium（Se）enrichment of rice under different rotation systems were studied，in order to identify the better types of winter green manure，and provide theoretical basis for the application of seleniumenriched paddy soil in Guangxi. Three types of rotation system were conducted，including Astragalus smicus-rice rotation （T1），Brassica napus-rice rotation（T2）and Raphanus sativus-rice rotation（T3），with winter fallow-rice rotation（CK） as the control. The effects of different green manures on selenium absorption and accumulation，soil available selenium，rice growth，and selenium content in rice were systematically analyzed. The results showed that there was a significant positive correlation between the total accumulation of selenium in green manure and the available selenium content in the soil during the period of green manure tilling and rice maturity. Moreover，the selenium content in rice grains was significantly positively correlated with the available selenium in the soil during the rice heading stage. There were differences in the absorption and accumulation of selenium among different green manures，the total selenium accumulation was ranked as Astragalus smicus ＞ Brassica napus ＞ Raphanus sativus，the available selenium content in the soil showed the same pattern. Planting green manure in winter was beneficial to increasing the selenium content in rice. Compared to the control，selenium content in unpolished rice treated with T1，T2 and T3 increased by 57.7%，51.6% and 25.9%，respectively，however，there was no significant difference in the proportions of organic selenium. It could be seen that the accumulation of selenium in green manure affected the available selenium content in soil，which could affect the selenium absorption by rice. Planting of Astragalus smicus in winter was more beneficial for increasing the available selenium content in selenium-enriched paddy soil，and increased the selenium content in rice in the subsequent rice growing season.