The intergrowth stage is a key stage of the winter wheat and cotton relay intercropping, which is not only important for the crop growth and yield but also for the quality of winter wheat. The effects of soil moisture on the yield and quality of wheat in the intergrowth were researched with the wheat and cotton relay intercropping in pattern 3:1(three lines winter wheat intercrop one line cotton) and pattern 4:2(four lines winter wheat intercrop two lines cotton). The research results reveal that the soil moisture prominently impacts the daily variation kinesis of transpiration rate and the daily net photosynthetic rate of wheat leaves. The highest yield of the winter wheat is produced from the 70% soil moisture. If the soil moisture is higher than 70%, it is helpless for the accumulation and distribution of the dry matters to the seed. Also the lower soil moisture treatment promotes the protein and wet gluten content of the wheat grain. The winter wheat of pattern 3:1 is easy to be restrained from the deficit of water.