The aim of this study was to analyze the effects of the microbial community structure in the rhizosphere soil of Haloxylon ammodendron on parasitism by Cistanche deserticola. The microbial community structure and arbuscular mycorrhizae (AM) fungal species were determined in samples collected from May 2013 to August 2013 by chloroform fumigation-extraction, phospholipid fatty acid (PLFA) analysis, and wet sieving and centrifugation methods. These findings were then used to reveal the relationships between parasitism by C. deserticola, the microbial community of H. ammodendron and environmental factors. The results showed that species diversity and the overall quantity of microbial cells were significantly more abundant than in August, and that the PLFA content and total number of AM fungi were higher in samples collected in June. The PLFA concentration data were subjected to principal component analysis (PCA), and the first two principal components (PC1, PC2) accounted for 90.12% and 9.21% of the total variation, respectively. This confirmed that the soil microbial community of H. ammodendron changed significantly during growth between May and August. Specifically identified PLFAs, including fatty acids that represented bacteria and fungi, were distributed on the right side of the load diagram, while fatty acids that represented actinomycetes were distributed on the left side of the load diagram. Thus, these results indicate that during H. ammodendron growth, total PLFA, PLFA representing bacteria and fungi, and PLFA representing actinomycetes all decreased from May to August. Thirty-five species of AM fungi from four genera were identified using the wet-sieving and centrifugation method. These included 22 species of Glomus, seven species of Acaulospora, three species of Diversispora, and three species of Gigaspora. The dominant species were Glomus melanosporum and Acaulospora bireticulata. The number of AM fungal spores, calculated using the counting method, was highest in June and lowest in May. The Gigaspora genus, which may participate in the parasitic process of C. deserticola, was found in the rhizosphere of H. ammodendron. We also found that the seed germination rate (65.94%) and parasitic rate (59.19%) of C. deserticola were significantly higher in June than in the other months, by seed germination and field parasitic experiments, respectively. Correlation analysis showed that the variations in the soil microbial community of H. ammodendron were mainly influenced by soil moisture and temperature characteristics. The quantity of fungi, which may affect the parasitic process, was significantly positively correlated with the soil temperature, indicating that during H. ammodendron growth and conditions of temperature increase, the PLFAs representing fungi increased. Furthermore, the germination rate and parasitism rate of C. deserticola were significantly negatively correlated with the 50 cm soil temperature and soil nutrients, indicating that during conditions of increased soil temperature and nutrient elements, the parasitism rate of C. deserticola increased. In conclusion, we speculate that there is a strong correlation between soil microorganisms in the H. ammodendron rhizosphere and the parasitic rate of C. deserticola. These findings provide deeper insight into the parasitic relationship between C. deserticola and H. ammodendron.