This study aimed to explore differences in the low-temperature tolerance of a desert plant, Anabasis aphylla, at different seed germination stages during the fall using transcriptome sequencing to identify related genes. The survival rate of the seeds decreased with lower temperatures at different germination stages, and the tolerance of the stages in decreasing order was as follows: imbibition (I) ≈ testa rupture (II) > testa removal (III) > elongation (IV). Superoxide dismutase, peroxidase, and catalase activities and the malondialdehyde content showed a downward trend after stage II. Transcriptome sequencing of seeds, including ripe and dry dominant seeds (W1) and seeds during different germination stages [imbibition (W2), testa removal (W3), and elongation (W4)] was performed. Some genes were downregulated during seed germination, which mainly included cytochrome P450, oleosin, ethylene-responsive transcription factor, and low temperature-induced protein. This study suggests that downregulated of some genes may result in a decrease in low-temperature tolerance.