The objective was to provide a scientific basis for using saline water for irrigation more effectively and reasonably. It was focused on the effects of two types of alternate irrigation regimes (alternating groundwater and saline water (GW-SW), and alternating groundwater, followed by two cycles of saline water (GW-SW-SW)) between three levels of irrigation water salinity (i.e. mineralization of 2.0g/L, 3.5g/L and 5.0g/L) and groundwater (1.1g/L) on soil moisture and saline distribution. The maize stem water uptake was investigated by detecting the stable hydrogen and oxygen isotopes of soil water and maize stem water, and the maize yield was calculated. The results showed that with the same depth of soil, soil moisture and EC were increased with the increase of irrigation water salinity, and were higher in the GW-SW-SW regime. The trend of soil moisture as depth increasing for all treatments at different periods were similar, but it was decreased at shallow depth and then increased at deep depth. The trend of soil EC as depth increasing for all treatments at the jointing and heading stage were similar to that of soil moisture; however, at the filling stage, the trend of soil EC as depth increasing for all treatments, it was increased at shallow depth, and then decreased as depth became deeper, and finally increased at deep depth. Based on the interception of curves for δ18O in soil water and maize stem water as shown, the specific soil depth values of maize stem water sources for each treatment were from 20.1cm to 26.1cm at the jointing stage, from 24.1cm to 63.0cm at the heading stage and from 11.0cm to 63.9cm at the filling stage, respectively. Except for the jointing stage, there were more than one soil depths for maize stem water sources for most treatments at the heading and filling stages. Based on the multiple linear mixed model (IsoSource), the main water absorption depths for all treatments were 0~20cm, 20~40cm and 0~20cm with the average contribution rate ranging from 33.9% to 51.0%, 27.4% to 83.0% and 32.0% to 80.6% at the jointing, heading and filling stages, respectively. The average contribution rate of the main water absorption depth in all periods was decreased with the increase of irrigation water salinity, and the average contribution rate of the GW-SW-SW regime was lower. The 2.0g/L salinity under the GW-SW regime showed the highest yield of 1.54kg/m2, which was 26.23% higher than the lowest yield in the 5.0g/L salinity under the GW-SW-SW regime. 