In order to comprehensively understand the utilization characteristics of soil microbial carbon of native coastal wetlands, topsoil (0-20 cm) in native coastal wetlands were treated by three simulated nitrogen deposition levels and the characteristics and variation of microbial functional diversity were analyzed by Biolog microplate method. The results showed that there were significant differences in functional diversities of microbial communities under different treatments and AWCD increased with the extension of incubation time along; Shannon and Mcintosh diversity indexes increased first with nitrogen increasing, and the diversity indices were significantly different under different treatments; Species diversity and functional diversity showed the same variation. The utilization intensities of carbon sources of six categories had differences in which the carbohydrates were the most dominant carbon sources. Principal component analysis (PCA) identified that soil microbial carbon utilization had obvious spatial differentiation under different wetland types, horizontal zone difference of soil microbial functional diversity was reflected in the use of carbohydrates, amino acids and amine, and the amine was particularly prominent. In addition, the correlation analysis between microbial diversity and soil physiochemical properties showed that total nitrogen, nitrate nitrogen, total phosphorous had significant impacts on soil microbial composition and functional activity in native coastal wetlands.