To investigate the effects of water regimes on yield formation, photosynthetic characteristics and transpiration efficiency of rice plants in arid region, plot experiments were conducted in 2011 and 2012 in Shihezi City with three water treatments, including flooding irrigation (W1), controlled irrigation technology (W2) and aerobic rice (W3). The results showed that there was no significant difference for net photosynthetic rate (Pn) in W1 and W2 treatments before anthesis, but W1 treatment was 11.29%~20.91% higher than W2 treatment, and 38.65%~52.03% higher than W3 treatment after anthesis across both years. Further analysis indicated that little difference of the parameters of Pn, carboxylation efficiency, saturation light intensity, and compensation light intensity were existed in W1 and W2 treatments in saturated soil moisture, the lower Pn in W2 and W3 treatments than that in W1 treatment was mainly due to significantly decreased Pn in W2 and W3 treatments when soil water content was unsaturated in 2011 and 2012 （p＜005). Moreover, the diurnal changes of Pn was higher in W1 treatment than that in W2 and W3 treatments during whole observed times, and the difference was greater on forenoon (before 12:00) than on afternoon (after 14:00) among treatments. Finally, the grain yield in W2 and W3 treatments only decreased by 4.43%~18.72% and 31.23%~39.45% when compared with W1 treatment considering both years. The transpiration efficiency in W2 treatment was always significantly greater than that in W1 and W3 treatments during whole growth stages in both years （p＜005). Generally speaking, the W2 treatment performs high grain yield and high water use efficiency in arid region, meanwhile, the grain yield in W2 treatment could be increased when improving photosynthetic produce ability in the afternoon at grainfilling stage.