Rape multiple-cropping is an important planting mode to promote grain stabilization and rapeseed increase in South China rice growing area. We explored the influence of soil organic carbon (SOC) accumulation and its stability characteristics under different rice-rape rotation measures with whole-straw returning, which is of great significance for in-depth analysis of soil carbon cycle in paddy fields by making full use of winter fallow fields to plant rape. This study is based on an 8-year yield localization experiment. In contrast with rice-rice-winter fallow, we explored the characteristics of SOC and its fraction accumulation under three rice-rape rotation treatments: rice-rice-rape, rice-rape-tillage, and rice-rape-no tillage. The results indicated that the content of SOC in 0~20 cm soil layer was increased by 5.28%~25.12% under the three rice-rape rotation treatments, especially under the rice-rice-rape treatment. Also, the increasing rate of SOC in 20~40 cm soil layer was 18.48%~43.97%, among which the rice-rape-tillage and the rice-rape-no tillage treatment reached a significant level. Except for rice-rape-tillage treatment in 0~20 cm soil layer, the content of mineral-associated organic carbon (MAOC) from all the rice-rape rotation measures was increased significantly in different soil layers. At the same time, the ratio of particulate organic carbon (POC) to SOC was significantly decreased while the ratio of MAOC to SOC increased in each treatment from both 0~20 cm and 20~40 cm soil layer. The increasing rate of MAOC/SOC were 2.31%~7.49% and 1.56 %~2.66% in the two soil layers, respectively. Possible causes of these results may be that rice-rape rotation increased the activity of organic carbon invertase enzyme (β-glucosidase、β-1,4-glucanase and Laccase) as well as microbial biomass carbon in 0~20 cm soil layer to varying degrees, thereby promoting the conversion of POC to MAOC. In summary, rape multiple-cropping in winter fallow not only promoted the accumulation of SOC in paddy field, but also increased the ratio of MAOC/SOC, ultimately enhancing the stability of soil carbon pool.