In oasis irrigation region of northwestern China, the decreasing of multiple cropping areas may lead to significant reduction of land and light use efficiencies due to serious water shortage. Therefore, water-saving irrigation is a priority in the research on theory and technology for intercropping system. Alternate irrigation is a technique to save water and enhance water use efficiency (WUE) simultaneously in common cropping systems. However, its effect is not clear on intercropping system. In 2006-2008 cropping years, we carried out a field experiment in oasis region of Hexi Corridor, Gansu province, China under wheat/maize intercropping to disclose the effects of alternate irrigation on crop yields, water consumption, and WUE. The results showed that, compared to sole cropping treatments, there was a significant increase of land equivalent ratio (LER) in the alternately irrigated wheat/maize intercropping treatment with the LER values ranging from 1.22 to 1.52 under different irrigation levels of the intercropping treatments. However, the difference of LERs between conventionally irrigated and alternately irrigated intercropping systems was not significant at the same irrigation quota. Compared to the conventionally irrigated intercropping treatment, there was no significant change of wheat yield in the alternately irrigated intercropping treatment, but significant increase by 11.4-36.4% in maize yield. Therefore, the total yield of wheat and maize in the alternately irrigated intercropping treatment was increased by 12.9 averagely. The water consumption in the alternately irrigated intercropping treatment had no significant increase compared to that of the conventionally irrigated intercropping treatment, with 1.2-19.4% higher than the weighted average of monoculture of both crops. The WUE of alternately irrigated intercropping treatment was 0.9-22.5% higher than that of the conventionally irrigated intercropping treatment, and 12.0-71.4% and 10.6-37.8% higher than that of wheat and maize monoculture, respectively. These results suggest that alternate irrigation is feasible in intercropping systems in arid oasis regions with the purpose of saving water and increasing WUE.