Agroforestry is a common traditional practice in China, especially in Southern Xinjiang, Northwest China. However, the productivity of many agroforestry systems has been lower than expected in recent years. We chose an apricot (Prunus armeniaca L.)/wheat (Triticum aestivum L.) intercropping system to investigate the influence of apricot tree shade intensity on the grain yield and quality of intercropping wheat in Southern Xinjiang Province. We found that the mean daily light intensity in the east-row, inter-row, and west-row positions (apricot trees were planted in north-south orientation) in the intercropping systems decreased by 61.5%, 42.2%, and 63.6%, respectively, compared to the monoculture wheat. Correspondingly, the mean daily photosynthesis rate decreased by 52.0%, 28.4%, and 38.8%, respectively. The total florets, fertile florets, total spikelets, fertile spikelets, and grain yield and its components (including spike number, grains per spike, and thousand grain weight), and the total N and P contents of intercropping wheat in apricot-based intercropping systems were all significantly decreased compared to monoculture wheat. However, the protein content and wet gluten content of intercropped wheat were significantly increased compared to monoculture wheat. We did not find significant differences in any parameters among east-row, inter-row, and west-row positions in intercropping systems.