Abstract: In order to use the mineralized shallow groundwater to relieve the crisis of freshwater resources shortage, the 5 years field experiment under border irrigation with mineralized water before sowing was conducted. The response relations among different salt stress levels and cotton growth index and seed cotton yield were analyzed in this study, and the cotton salt tolerance appraisal indices and eigenvalue under border irrigation with different saline water before sowing were put forward. The results showed that the relative emergency rate, relative plant height, relative leaf area, relative above-ground dry matter mass, relative fruit branch number, relative boll number and relative maximum of buds, flowers and bolls all could be used as salt tolerance appraisal indices of cotton. The relative height was recommended as the most practical salt tolerance appraisal index among them because it was easy to observation and sensitive to salt stress. The salinity of irrigation water should be below 5.48 g/L when the yield of seed cotton in saline water treatment was consistent with the fresh water irrigation treatment after a 5- year continuous irrigation.