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Effects of tree shading on crop within agroforestry system in the oasis regions or under irrigation agriculture are poorly understood. Objective was to determine maize yield variation and its reasons when tall Poplar trees (Populus gansuensis) were grown in western and eastern margins of the crop field in Hexi Corridor desert oasis in northwestern China. Maize growing among the 50 m alley space were divided into five regions, including shading region in western side (W-S), non-shading region in western side (W-NS), middle region (M), shading region in eastern side (E-S) and non-shading region in eastern side (E-NS), for all measurements. Measurements of leaf area expansion were carried from seeding to flowering stage, photosynthetic physiological parameters and microclimate characteristics were measured at booting stage, grain yield and other harvest parameters were obtained at harvest time. We found that tree shading reduced the crop yield by 27 and 22% in western and eastern regions, respectively, and also, mean crop yield for western side was 23% lower than eastern side. The direct reason of yield variation was transpiration rate (E) variation at booting stage, that is, maize which had higher daily mean E would obtained higher yield. Moreover, changes of incident photosynthetically active radiation (PARi), air temperature (T (a)) and CO(2) concentration (C (a)) were the basic reasons of yield variation among different regions. Because higher PARi, higher T (a) and lower C (a), which caused by the tree shading, would all led to higher E and finally higher crop yield.