Soil health is important of the sustainable development of paddy soil ecosystem. In this study, the relationship between soil quality and microbial properties, enzyme activities in reddish paddy soil (a Typic Haplic-Stagnic Anthrosis) was studied in order to illustrate the microbial properties as the indicators of soil health. Microbial parameters with different winter-planting green manure experimental plots were analyzed based on a 26-year of long-term experiment in the Key Field Monitoring Experimental Station for Red Soil Eco-environment of Ministry of Agriculture, Qiyang County of Hunan Province, China. Four treatments were established in 1982, i.e., rice-rice-winter fallow (R-R-WF), rice-rice-rape (R-R-RP), rice-rice-Chinese milk vetch (R-R-MV), rice-rice-ryegrass (R-R-RG). The results showed that the amounts of microbial population, microbial biomass carbon (SMBC), microbial biomass nitrogen (SMBN), soil respiration, activities of urease, lnverstase and dehydrogenase increased and metabolic quotient (qCO2) decreased in long-term winter planting green manure incorporation treatments. The microbial characteristics in treatments with long-term winter planting green manure incorporation were significantly improved as compared with the winter fallow treatment; all these properties in treatment with winter planting Chinese milk vetch were most obvious. In the meantime, the amounts of microbial populations, SMBC, urease and dehydrogenase were positively correlated with TOC, TN, AN, SLK and AK; TOC, TN, AN, SLK, AK, bacterium, fungi, actinomycetes, urease, lnverstase and dehydrogenase were positively correlated with rice yield. Long-term winter planting green manure incorporation could significantly improve soil microbial properties and enzyme activities, which is an effective measure to improve soil health and soil fertility in the Typic Haplic-Stagnic Anthrosis.