The effects of wetting and drying on paddy soil carbon (C) and nitrogen (N) mineralization were investigated by soil microbial biomass and physical-chemical condition under different long-term fertilizer treatments with incubation experiments. Results indicated that compared with continuous wetting (CW) period, not only did C mineralization rate in drying period with drying and wetting (DW) increased by 78% ~ 204% for all the soils, but also soil microbial biomass C and N increased by 55% ~ 77% and 57% ~ 72%, respectively. In rewetting period C mineralization rate increased by 74% ~ 95%, with the trend of decrease followed increase. N mineralization rate in rewetting period increased by 21% for NPK, while it decreased by 5% and 13% for CK and NPKOM, and it decreased by 34% ~ 78% in drying treatment for all the fertilizer treatments. During incubation period, soil Eh value in the range of -60 ~ 60 mV had negative correlation with soil microbial biomass C (SMBC). In the process of drying with DW, pH value increased with soil microbial biomass C growth. In the wetting period, pH value was negatively correlative with soil microbial biomass C only in NPKOM treatment. Further research is needed to assess the interactive correlations between C and N mineralization, Eh and pH value, and soil microbial community and biomass under the alternative flooding and drying cycles because they are complex and intricate.