Based on the 2-year experiment，four fertilization treatments(organic fertilizer； organic fertilizer plus 2 000 kg·hm -2green manure； organic fertilizer plus 3 000 kg·hm -2green manure； organic fertilizer plus 4 000 kg·hm -2 greenmanure)were established to investigate their effects on soil organic carbon fractions and the rice yield. The results showed thatcompared with organic fertilizer alone(OF)，no significant differences on soil and aggregate organic carbon concentrationswere seen under the three treatments with green manurereturn，while the rice yield was significantly increased. With aggregates of 0.25～2 mm divided into three fractions，it was found that the organic carbon concentration increasedwith the increase of their particle size. Compared withOF，green manure return significantly increased organic carbon concentrations within the 0.05～0.25 and < 0.05 mm fractions，which was probably caused by changes of the free lightfraction，demonstrated through the density floating experiment. Correlation analysis showed that the rice yield was positively correlated with organic carbon concentrations within the 0.25～ 2 mm aggregates and within the 0.05～ 0.25 mm fraction.Green manure return could indirectly affect the rice yield by increasing organic carbon concentration within the 0.05～ 0.25mm fraction. Therefore，during the clean production(organicproduction)ofrice，it is recommended to combine organic fertilizer with green manure to improve the rice yield and soil fertility and the application rates of green manure could be from3 000～ 4 000 kg·hm -2 accordingly.