In South China, application of winter green manure crops into the double rice cropping system has been proved to be a high effective rotation pattern in improving soil environments, soil fertility and rice yields，and is very beneficial to the sustainable agriculture. The effects of long-term application of green manure crops on soil microbial biomass carbon, soil microbial biomass nitrogen and the seasonal fluctuation of soil microbial biomass properties in red paddy soil were still not clear enough. Based on a 31-year long-term field experiment on cultivation of double cropping rice and winter green manure in red paddy soil in South China, soil microbial biomass properties were investigated at different stages, aimed to provide a theoretical basis for deliborating mechanism and effects of winter green manure on transformation of soil carbon and nitrogen in the paddy ecosystem. The long-term field experiment includes 4 treatments, i.e., rice-rice-milk vetch (RRV), rice-rice-winter rape (RRP), rice-rice-ryegrass (RRG) and rice-rice-winter fallow (RRF). Soil samples were collected at 4 different typical stages, i.e., flowering stage of winter green manure crop (S1), after the incorporation of green manure (S2), mature stage of early rice (S3), and after the harvest of late rice (S4), for analysis of soil microbial biomass carbon (SMBC), soil microbial biomass nitrogen (SMBN), soil microbial quotient and soil microbial biomass carbon to nitrogen ratio (SMBC/SMBN). The results showed that the cultivation of green manure crops increased the contents of SMBC, SMBN and soil microbial quotient. Especially at the S4 stage, when soil properties were relatively stable, all the green manure treatments were significantly higher than those in the RRF treatment, and similar trends were observed for the annual mean values. The SMBC and SMBN were most influenced by the leguminous green manure milk vetch. Compared with the RRF treatment，they were increased by 21.12% and 98.45%, respectively, at the S4 stage, and by 15.92% and 3.49% for the annual mean values, respectively. The annual average values of soil microbial quotient in RRV, RRP, RRG were 3.61%, 3.66% and 3.61%, respectively, significantly higher than that in RRF treatment (3.13%). Although the SMBC, SMBN and soil microbial quotient were affected by sampling time profoundly, they all showed similar trends at all the 4 sampling stages, i.e., no significant differences between the stage of S1 and S2, down to the lowest level at the S3 stage, and up again at the S4 stage. The SMBC to SMBN ratio did not vary much among different treatments but fluctuated obviously with the sampling stages, i.e., highest at the S3 stage (when soil being flooded) and lowest at the S4 stage (when soil being non-flooded). It could be concluded that soil microbial properties were improved obviously after the long term cultivation of winter green manure crops in red paddy soil in South China, furtherly supporting that the cultivation of winter green manure crops is an effective way for soil fertilizing in red paddy fields.