China is one of the countries most severely affected by desertification. Haloxylon ammodendron is an ecologically important component of the desert ecosystem and is one of the main shrub species used for ecological restoration. We compared the genetic variation in seed and seedling traits among six H. ammodendron provenances arrayed from east to west in China. The experiment was carried out in a greenhouse in well-prepared seedling beds (lines 1.5 m apart and seeds with in lines 1.0 m apart, 2.0 cm deep) with five lines (seven seeds per line) per provenance in a randomized block design with six replicates. The seed traits of fruit wing length, kernel weight, germination rate, and survival rate were compared, as were the seedling traits of internode length, branch number, assimilation shoot diameter, height, collar diameter, new shoot length, main root number, main root length, aboveground fresh weight, and underground fresh weight. Moreover, correlations between each seed and seedling trait and climate and geographical factors were assessed. The results show that the seeds from Dengkou County, Inner Mongolia had the best performance. Germination rate and survival rate were significantly positively correlated with longitude; and fruit wing length, kernel weight, seedling height, and new shoot length were significantly negatively correlated with latitude. Fruit wing length was significantly correlated with altitude. Among the climatic factors, the temperature in January had a strong direct effect on fruit wing length, germination rate, seedling height, and new shoot length. The mean annual rainfall had a strong direct effect on collar diameter. Humidity had a strong direct effect on survival rate. Seedling height, aboveground weight, and collar diameter could be important criteria for early provenance selection in the seedling stage. This study provides a reference for the selection of high-quality H. ammodendron seeds for drylands of northwest China.