Abstract: The area of brackish water irrigation has become increasingly year by year. Soil environment has been polluted in different degrees by illogical irrigation. In this paper, the effects of brackish water irrigation on the environment factors of soil-crop system under different groundwater depths were studied. The experiment was carried out in a lysimeter. The results showed that salinity accumulation did not appear in 0-100 cm soil layer when irrigated by saline water in the area of groundwater depth below 3 m. The effect of irrigation water quality on soil salinity was more significant than groundwater depth when salt concentration of irrigation water was 4 g/L. The deeper the groundwater depth was and the higher the salinity level was, the less the leaf area index, height of plant and yield were. And the effect of groundwater depth on morphological index was more significant than salinity level.