Artemisia annua L., widely distributed in Southwest China, is the sole plant source of artemisinin. To understand the mechanism of resistance to desert about this medicinal plants for higher yield and quality of artemisinin, researches were done to study nutrients and microorganisms in soils where wild A. annuagrew. Results show that the soils at different sample sites varied greatly in organic matter, nutrients, pH, enzyme activity and population of microbes, suggesting that A. annua is tolerable to either high or low soil fertility and hence highly adaptable to a variety of habitats. In soil analysis, 24 kinds of phospholipid fatty acids (PLFAs), biomarkers of soil microbes, were detected with a gas chromatograph-mass spectrometer (GC-MS), including 19 kinds of PLFAs with 11~19 carbons (C), biomarkers of bacteria, 10Me18:0, biomarker of actinomyces, 18:2ω6,9, 18:1ω9c and 18:1ω9t, biomarkers of fungi, and 20:0, biomarker of nematode. And in terms of total amount of PLFAs, the sequence of bacteria > actinomyces> fungi was found. In the rhizosphere of A. annua, pH was obviously lower than in the bulk soil, but contents of organic matter, alkalystic N, available P, readily available K, microbial C and N, and FLFAs, activities of sucrase, urease and phosphatase, and indexes of diversity and homogeneity of microbial colonies were just the otherwise. Rhizosphere microorganisms were closly involved in transformation of N and P in the soils. In addition, total PLFAs in soil microbes were significantly and positively related to plant biomass and yields of artemisic acid and artemisinin, and so were soil microbial biomass C and N to yield of artemisinin, The study provides evidence that it was suitable for growth of various species of microorganisms, high density and enzyme activities in rhizosphere soil of wild A. annua, so effectiveness of the soil nutrient improved was beneficial to the wild A. annua adapted to different soil conditions and that the existence of soil microorganisms significantly affects growth and contents of effective component of wild A. annua .