Haloxylon ammodendron, a chenopodiaceae shrub species that mainly distributes in northwest of China, is an ecologically important foundation species and exhibits substantial low-temperature tolerance in the desert area. We employed RNA-Seq technologies to identify genes involved in low temperature, and identified 17995, 15511 and 1550 differentially expressed genes from the comparison of chilling treatment versus control, freezing treatment versus control and freezing treatment versus chilling treatment, respectively. By performing BLAST analysis of these unigenes against public databases, "single-organism metabolic process" and "membrane" were strongly affected at low temperature, and "Plant hormone signal transduction" pathway played an important role in resistance of the plants. In addition, we analyzed transcription factors, and found 499, 453, 55 of them were differentially expressed in these three comparison groups, respectively. A large number of transcription factors were identified at low temperature, and six transcription factors were selected for further expression analysis using qRT-PCR. This study can understand the molecular mechanisms of Haloxylon ammodendron at low temperature condition, and also can serve as a valuable resource for relevant research on low-temperature tolerance.