In order to study the tolerance of different lotus varieties to saline-alkali stress and to screen resistant varieties, using pot culture method, 20 lotus varieties were used as experimental materials, and 100 mmol·L-1 (NaCl∶NaHCO3=2∶1) hybrid saline-alkali stress treatment, 7 d after measuring the plant height, leaf area, photosynthetic pigments, chlorophyll fluorescence parameters, content of malondialdehyde, activity of antioxidant enzyme and content of osmotic regulatory substances, the saline-alkali tolerance of 20 lotus species was evaluated comprehensively by means of saline-alkali tolerance coefficient, correlation analysis, principal component analysis, membership function method and cluster analysis. The results showed that there were significant differences in the variation coefficients of saline-alkali tolerance among different lotus varieties. Except superoxide dismutase activity and peroxidase activity, the saline-alkali coefficients of other single indexes were significantly or extremely significantly correlated. The 12 single indexes were converted into 5 comprehensive indexes by using principal component analysis. The contribution rates of each comprehensive index were 36.175%, 18.709%, 13.470%, 11.379%, 6.610%, and the cumulative contribution rate reached 86.344%. With saline resistance value (D value) based on clustering analysis, 20 lotus varieties could be divided into four categories, first, there was strong salt-tolerant type, a total of four lotus varieties, and the second category of salt-tolerant type, a total of five lotus varieties, and the third category was not salt-tolerant type, a total of eight lotus varieties, the fourth category for sensitive type, a total of three varieties of lotus. The optimal evaluation model of salinity and alkali tolerance of lotus was established by stepwise regression analysis, D=0.453+0.148X1+0.122X2-0.122X7-0.033X8+0.093X11+0.037X12(R2=0.992), and the estimation accuracy was above 95.45%. Plant height, leaf area, malondialdehyde, proline, soluble sugar and soluble protein were selected as evaluation indexes of the saline-alkali tolerance of lotus. The saline-alkali tolerance of lotus could be determined by measuring these 5 indexes under the same conditions.