Gymnocarpos przewalskii is a rare Tertiary relict species found in the desert regions of Central Asia; the natural population distribution of G. przewalskii is declining owing to climate change and human interference. As an important life history stage of plants, seed dispersal is not only critical for the survival and diversity of species, but also affects the distribution and local abundance of species. In 2015 and 2016, seed traps were installed around G. przewalskii mother plants in different directions in Hami. The spatial and temporal dynamics of seed dispersal of this natural population were continuously observed. The results showed that seeds began to disperse in early June and seed dispersal in 2015 was slightly earlier than in 2016. Seed dispersal lasted about 2 months; the dispersal trend was a single peak curve and presents a pattern of mass dispersal. The peak of seed dispersal coincided with the peak of the first monthly precipitation of the year. Dispersal occurred at the highest density and for the longest distance south and southeast of downwind. The seeds were mainly concentrated directly underneath the canopy of the mother plant. As the distance from the mother plant increased, seed density decreased, and there was a very significant negative correlation between dispersal distance and dispersal density. The main reason for the high dispersal density of seeds of G. przewalskii under the mother plant is that its numerous branches weakened the wind strength through the plants. Seed dispersal of G. przewalskii was affected by precipitation, wind, and plant characteristics. Seed dispersal before heavy precipitation may be beneficial for seed germination in suitable microhabitats, which is a long-term adaptation of G. przewalskii to the harsh wind and drought conditions.