Nitrogen fixation, nitrification and denitrification are three important ecological processes in soil nitrogen cycling, and they are mainly driven by soil microorganisms. The recent progresses in relation to the relationships between soil nitrogen cycling and soil functional microorganisms are reviewed in this paper. Firstly, soil nitrogen-fixing bacterial communities have been studied using nifH gene molecular marker. A significantly positive correlation between soil organic matter content and the abundance and composition of the nitrogen-fixing community was observed. The abundance and diversity of the nitrogen-fixing community were declined due to the application of nitrogen fertilizers. Secondly, the corelations between soil characteristics and soil nitrifiers was intensively investigated. Results indicated that ammonia-oxidizing archaea (AOA) played a leading role in nitrification in acid soils, whereas the ammonia-oxidizing bacteria (AOB) played a key role in nitrification in cultivated and alkaline soils. Application of nitrogen fertilizer increased the copy numbers and activities of ammonia oxidizing microorganisms. Thirdly, the effect of environmental factors on soil denitrifiers was also researched, it was demonstrated that soil dissolved organic carbon, pH and soil water content were the key factors affecting the population size and community composition of soil denitrifying bacteria. It was further suggested that the composition and abundance of soil denitrifiers were closely associated with soil denitrification potential and N2O emmissions in ecosystems. In the future, as some new technologies introduced into soil microbial ecology, such as isotopic tracer, soil nitrogen cycling molecular mechanisms would be more clearly explored.