Freezing and thawing cycles (FTCs) significantly changed the soil microbial activity and carbon and nitrogen cycling processes. A laboratory freezing-thawing stimulating experiment was conducted using 0-15 cm and 15-30 cm soil samples from Jinchuan peatland in Changbai Mountain. Two FTC amplitudes, namely, -10-10℃ and -5-5℃, were tested. Soil microbial biomass and phospholipid fatty acid (PLFA) concentrations were analyzed using chloroform fumigation method and phospholipid fatty acid method, respectively. Soil properties were analyzed after 0, 1, 3, 5, 7, and 15 cycles and compared with the properties of FTC (0). Results showed that freezing-thawing cycle had significant effects on soil microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), and microbial phospholipid fatty acids (P<0.001). Soil microbial biomass carbon (MBC) increased significantly, but soil microbial biomass nitrogen (MBN) decreased compared with the FTC (0) after 15 FTCs. All groups of PLFAs concentrations dramatically decreased both in the -5-5℃ and -10-10℃ FTC amplitudes. The Freezing and thawing cycles significantly changed the soil microbial community structure with soil Fungi/Bacteria ratio decreasing (except -5-5℃, 0-15 cm soil) but Gram-positive bacteria/Gram-negative bacteria ratio increasing after FTCs. The effect of FTCs on soil microbial PLFAs under FTC amplitude of -5-5℃ was greater than that under the FTC amplitude of -10-10℃, but the opposite phenomenon was observed with respect to the effect of FTCs on MBC. The effect of FTCs on soil MBC and most groups of PLFAs were greater in the 15-30 cm than those in the 0-15 cm under the two FTC amplitudes. This indicated that the effect of FTCs on soil microbial biomass and microbial community varied with soil depth. The number of FTCs had a significant influence on soil microbial biomass and PLFAs (P<0.05). The results of correlation analysis showed that the different group of soil microbial PLFAs were positively correlated with the soil MBN concentrations (P<0.01) but negatively with the dissolved organic carbon (DOC) (P<0.05). In conclusion, freezing promotes the death of microorganisms and provides more carbon sources and nutrients for the survival of microorganisms in thawing period, which further changes the structure of soil microbial community. The decreasing of different groups of phospholipid fatty acids during freezing and thawing period may reduce the soil carbon sequestration capacity of peatland in this period.