Zygophyllum macropterum is a perennial herb that flowers in early spring and produces three types of fruits, which differ in the number of wings. To better understand how Z. macropterum has adapted to its desert habitat, its reproductive phenology, fruit morphs, fruit-set patterns, and germination characteristics were studied in a population in the Junggar Desert, Xinjiang, China. Vegetative budding of Z. macropterum occurred in early March, and its annual growth cycle lasted 4 months. The vegetative phase was 20-30 days, which accounted for a quarter of its annual growth cycle. Flowering in the population initiated in mid-April and peaked at the end of April, and the total blooming period lasted 45 days. The total reproductive phase was 90-100 days, of which the flowering period accounted for about one third to one half. Young fruits gradually formed during the full-bloom stage, and the mature fruiting phase lasted only 14-18 days. In early June, fruits began to crack and fall off, and the fruiting season lasted 80 days. After the fruits fell in mid-July, most of the ground parts of the plants dried, and the underground parts became dormant. Small autumn shoot sprouted at the base of the stem, and the lamina was small, pachyntic, and dark in color. The fruit of Z. macropterum is a capsule with membranaceous wings. The fruits hang pairwise in leaf axils and can be divided into three types based on whether they have three (Type 3 fruits), four (Type 4), or five (Type 5) wings. The three types differ in weight and in numbers of ovaries and seeds. Lighter fruits produce fewer seeds; hence, Type 3 and Type 4 capsules can easily disperse over a long distance by wind, whereas Type 5 fruits remain near the mother plant because of their weight. Depending on the types of fruit they produce, individual Z. macropterum plants are classified into Type 5 plants, Type 4/5 plants, and Type 3/4/5 plants, which occurred in the studied population at frequencies of 3.45%, 83.15%, and 13.40%, respectively. Additionally, depending on the number of growing stems, the plants can be considered class Ⅰ (< 20 stems), class Ⅱ (20-50 stems), or class Ⅲ (> 50 stems). As the mother plants increased in size, the ratio of three-winged fruits increased from 0% to 2.65%; Type 4 fruits have the largest proportion (17.01%) on class II plants. Type 5 fruits consistently were present in high proportion (> 80%), with the largest proportion (92.9%) found in class I plants. Seeds from all fruit types had similar germination characteristics and no significant differences in morphology. The seeds were physiologically dormant because the germination rate was low (< 30%) across a temperature range. Germination occurred slowly, and seed coat scarification of all three types of seeds could promote germination at different degrees. In conclusion, the phenotypic diversity of the fruits and reproductive phenology of Z. macropterum may be the result of its adaptation to the extremely harsh desert environment. Studying the reproductive phenology and fruit-set patterns of plants can greatly enhance our understanding of the mechanisms of adaptation to habitats and the evolution of plant life-history strategies.