How to make the water quality monitoring under the influence of high levels of salt, is the key to the effective management of water quality in oases in arid areas. The author takes Ebinur lake watershed as the study area, combining three-dimensional fluorescence excitation-emission matrices (3-DEEM) with parallel factor analysis (PARAFAC), extracting three -dimensional fluorescent components of surface water in Ebinur lake watershed, constructing the index of three-dimensional fluorescence spectrum, which is fit surface water in arid area, using linear regression were establishing diagnosis model of water salt content based on the technique of three-dimensional fluorescence spectrum. The results showed that: (1) The four fluorescence components were successfully extrapolated by the parallel factor analysis modeling from the fluorescence EEM data including microbial humic-like (Component 1), terrestrial humic-like organic substances (Component 2, Component 4), and protein-like organic substances (Component 3); (2) Three-dimensional fluorescence index analysis showed that terrigenous organic pollution was the main organic pollution type in the watershed. This study indicates that the watershed is subject to human disturbance, gives the large variation of organic pollution in the water body, and the correlation between three-dimensional fluorescence index, fluorescent components and water salt content is significant; There is a significant relationship between W2， W4， W7， F355， HIX, BIX and salt water content. The correlation coefficients r in the range of 0516 and 0915, is a negative relationship between BIX and water salt content, and the correlation coefficient r is -057. (3) The application of three-dimensional fluorescence index and fluorescence component to establish salt water content produced a model fitting coefficient (r) that is greater than 07 and residual predictive deviation (RPD) that is greater than 14, the model has a high predictive ability, which demonstrated that the accuracy of the model was in line with monitoring requirements in practice. Therefore, based on the three dimensional fluorescence spectrum technology, the realization of Ebinur Lake Watershed surface water salinity diagnosis research is effective. This study not only explores the three-dimensional fluorescence characteristics of the surface water of the Ebinur Lake Watershed, but may also be applied to three-dimensional fluorescence extraction of other surface waters in arid regions of Central Asia.