Seed germination profoundly impacts plant community composition within the plant life cycle. Snow is an important source of water for seed germination in the temperate deserts of Central Asia. Understanding how seed germination responds to variations in snow cover in relation to seed traits and plant ecological characteristics can help predict plant community sustainability and stability in Central Asia under a scenario climate change. This study investigated the seed germination of 35 plant species common to the Gurbantunggut Desert in Central Asia under the three snow treatments: (1) snow addition; (2) ambient snow; and (3) snow removal. Two-way analysis of variance (ANOVA) tests were performed to assess interactions among the impacts of snow treatments, seed traits and plant ecological characteristics on seed germination. Phylogenetic generalized least-squares (PGLS) model was used to test the relationships between seed traits and seed germination. The results demonstrated that snow variations had no significant impacts on seed germination overall. Seed germination under the snow addition treatment was similar with that under the ambient snow treatment, irrespective of seed traits and plant ecological characteristics. Snow removal only had negative impacts on seed germination for certain groups of seed traits and plant ecological characteristics. Seed mass positively affected seed germination, showing a linear increase of arcsin square root-transformed seed germination with log-transformed seed mass. Seed shape also profoundly impacted seed germination, with a higher germination percentage for elongated and flat seeds. Seed germination differed under different plant life forms, with semi-shrub species showing a significantly higher germination percentage. Most importantly, although snow treatments, seed traits and plant ecological characteristics had no interactive effects on seed germination overall, some negative impacts from the snow removal treatment were detected when seeds were categorized on the basis of seed mass and shape. This result suggests that variations of snow cover may change plant community composition in this temperate desert due to their impacts on seed germination.