Haloxylon ammodendron and Haloxylon persicum, belonging to the family Amaranthaceae, genus Haloxylon Bunge, serve as host plants for Cistanche deserticola. They are widely distributed in the arid zones of China. In this study, biological characteristics and agronomic traits of H. ammodendron and H. persicum were mainly compared by field observation and molecular identification. The results showed that there were significant differences in phenotypic characters, pollen structure and agronomic traits between H. ammodendron and H. persicum. Notably, the fruit wing length and assimilation branch length were significantly lower in H. ammodendron than compared to H. persicum. The pollen volume and surface particle structure of H. ammodendron were significantly smaller than those of H. persicum. Additionally, the pollen net of H. ammodendron exhibited a deep structure, while it was shallow and most of it protruding outwards in H. persicum pollens. The correlational analysis revealed significant positive correlations between the agronomic indexes of both H. ammodendron and H. persicum and climate factors such as temperature and humidity. Water and light are the primary limiting factors for the geographic distribution H. persicum in Junggar Basin of Xinjiang, while environmental adaptations of H. ammodendron were found to be stronger. H. ammodendron and H. persicum can be effectively identified by ITS barcode, and both of them can be parasitized by C. deserticola. However, the survival rate of C. deserticola were different. According to their biological characteristics, cultivating H. ammodendron is deemed suitable for the production of cistanches herba. This study provides a scientific basis for the identification and conservation of Haloxylon, as well as the selection of optimal hosts for C. deserticola.