The changes of soil C:N:P ratios and pH under nitrogen deposition, its effect on soil organic matter and litter decomposition and the possible soil microbial mechanism are the new position and scientific research front of terrestrial ecosystem and global change. The paper based on ecological stoichiometry and soil microbial ecology, summarized the basic theory, new advances, hot and difficult points of research on the effect of nitrogen deposition on soil organic matter and litter decomposition and the microbial mechanism, to advance the research of terrestrial underground ecology under global change. The continuing increasing nitrogen deposition accelerated the phosphorus cycling of forest ecosystem, caused phosphorus limitation. Nitrogen deposition not only changed soil organic matter and litter C:N:P ratios and decreased soil pH, but also changed soil microbial components of carbon, nitrogen and phosphorus, composition of bacterium, fungus and actinomycetes, the key enzymes for decomposition of carbon, nitrogen and phosphorus. The effects of nitrogen deposition on soil organic matter and litter decomposition have three states: motivation, suppression, no effect, the reasons for the different effect maybe come from different microbial effect. Leaves had obvious resorption of nitrogen and phosphorus, but root had less resorption rate, which caused clearly different C:N:P ratios between soil organic matter. The molecular methods based on DNA/RNA provided advanced tools for soil microbial ecology research,which would promote researches on microbial mechanism of soil organic matter and litter decomposition.