In the arid and semiarid regions, discrete precipitation pulses are important triggers for biological activity. Soil biogeochemical processes in these water-limited systems are closely linked to episodic rainfall events, and the relationship between microbial activity and the amount and timing of rainfall has important implications for carbon balance of the whole-system. In this paper the influence of rainfall on soil respiration was determined in field of natural deserts with Anabasis aphylla and Halostachys caspica in the western Junngar Basin, Xinjiang. The amount of rainfall was controlled at 5 mm and 2.5 mm with a control treatment (0 mm precipitation), respectively. A pattern of soil respiration rate after rainfall, that is, a decline followed by a subsequent increase which was followed by another decline was observed. Maximum soil respiration occurred at the 5 mm and 2.5 mm treatments lagged behind that for control treatment. The maximum rate and the declining respiration rate thereafter were higher at the 5 mm and 2.5 mm treatments than that at the 0 mm treatment. Soil respiration was influenced by temperature and soil moisture following rainfall. It was shown that the first decline of soil respiration coincide with wettest soil moisture at the 10th minute after rainfall, and the largest soil respiration occurred simultaneously with soil surface temperature at the 180th or 300th minute. The difference of soil respiration in three rainfall treatments was not significant for the two communities during 0-450 minutes following rainfall simulation. The average rate of soil respiration at the 5 mm treatment was largest in the Anabasis aphylla community, while that at the 2.5 mm treatment was largest in the Halostachys caspica community. The response of soil respiration to rainfall simulation is dependent on rainfall size, antecedent soil moisture condition and soil texture and so on.