Abstract: Wheat/faba-bean strip intercropping is a common intercropping system in Northwest China, which has significantly contributed to food security and poverty alleviation. However, traditional net irrigation quota for wheat/faba-bean intercropping is relative higher, deepening the conflict between water resources supply and demand in agriculture. The alternating irrigation is a biological water-saving technique that is extensively used in agricultural production in arid and semi-arid areas, which is assumed to increase WUE and maintain high yield in wheat/faba-bean intercropping system. In order to determine the effects of alternating irrigation on physiology response and yield of wheat/faba-bean intercropping, a root box experiment was conducted in glass greenhouse condition in Gansu Agricultural University in 2008. The experiment had two irrigation methods alternating irrigation (A) and conventional irrigation (T) and three planting patterns sole wheat (SW), sole faba-bean (SF) and intercropped wheat/faba-bean (IWF). The results showed that leaf chlorophyll content of intercropped wheat and faba-bean increased under alternating irrigation condition. On the contrary, leaf relative water content and leaf water potential decreased compared with conventional irrigation treatment. However, there were no significant differences between the two irrigation methods for wheat intercropped with faba-bean. Leaf chlorophyll content and leaf water potential of intercropped wheat were higher than those of sole cropping. Also leaf chlorophyll content, leaf relative water content and leaf water potential of intercropped faba-bean were significantly higher than those of sole faba-bean. Compared with conventional irrigation treatment, transpiration rate and stomatal conductance reduced by 10.99% and 6.66%, respectively, in intercropped wheat leaves, and by 6.78% and 5.32%, respectively, in intercropped faba-bean leaves under alternating irrigation conditions. Thus leaf water use efficiency of wheat/faba-bean intercropping under alternating irrigation improved. Compared with conventional irrigation, shoot dry weight of sole wheat, sole faba-bean, intercropped wheat and intercropped faba-bean decreased, while root/shoot ratio significantly increased under alternating irrigation. The root/shoot ratio of sole wheat, sole faba-bean, intercropped wheat and intercropped faba-bean in alternating irrigation treatments were 14.47%, 7.56%, 36.36% and 19.63% higher than those of conventional irrigation, respectively. Compared with sole cropping, yield of intercropping treatments generally increased. The harvest indexes of intercropped wheat under alternating and conventional irrigation increased by 8.68% and 2.72% over those of corresponding sole wheat treatment, respectively. Also harvest index of intercropped faba-bean under alternating and conventional irrigation increased by 4.78% and 5.23% over those of the corresponding sole faba-bean treatment, respectively. In conclusion, wheat/faba-bean intercropping under alternating irrigation maintained high leaf water use efficiency of wheat and faba-bean by increasing root growth and root/shoot ratio. It significantly reduced excessive transpiration without much reduction in photosynthetic rate. The research suggested that wheat/faba-bean intercropping under alternating irrigation had the potential for the realization of high-quality and efficient irrigation.