A 20-year field experiment on fertilization models, e.g. applications of inorganic fertilizer alone (CF) and inorganic fertilizer combined with wheat straw (CF/OM) was carried out to study responses of the soil in microbial abundance and enzyme activity in the National Field Research Station of Desert Ecosystem in Fukang, Xinjiang, China. Real-time quantitative polymerase chain reaction (Real-time PCR) analysis indicates that the abundances of soil ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were significantly higher in Treatment CF and Treatment CF/OM than in the control (no application of fertilizer, CK). The population of soil AOB was increased at least by 16 times while that of soil AOA at best by 3 folds, which suggests that AOB play a more important role in in-situ nitrification. Although Treatment CF/OM did not differ much from Treatment CF in crop yield, but was the highest in population size of main soil microbial groups, content of soil organic carbon and activity of most soil enzymes when still sustaining crop yield, which indicates that combined application of chemical fertilizer and organic manure is conducive to maintenance of soil micro-biodiversity and plays an important role in improving soil quality for sustainable agriculture.