Future climate change scenarios indicate the changes in duration and amount of rainfall. Rainfall is the most important water resources for arid and semi-arid area, and the changes in rainfall patterns will directly affect the stability of arid and semi-arid ecosystems. Soil microbe has been used as a sensitivity index to monitor the stability of eco-systems. This paper reviewed the direct effect of rainfall on the biomass and diversity of soil microbe in arid and semi-arid areas, and the indirect effect on soil microbe by changing the soil moisture, soil air and vegetation growth, which are also accompanied by interference from other factors, such as land use patterns, temperature, altitude, etc. We can better predict the inference of future climate change on the ecological stability in arid and semi-arid areas by understanding the impact of rainfall on soil microbe of the same region. Based on the current research, this paper summarized the existing problems and also prospected the future studies on the effect of rainfall on soil microbe in arid and semi-arid area.