[Objectivc] This study aimed to investigate the chilling tolerance of seedlings of different cotton genotypes and screen appropriate indicators for assess- ing chilling tolerance, to establish reliable mathematical evaluation model for chilling tolerance of cotton, thus providing theoretical basis for breeding and promoting new chilling-tolerant cotton germplasms and large-scale evaluation of chilling tolerance of cotton varieties. [Method] Fifteen cotton varieties (lines) were used as experimental materials. The photosynthetic gas exchange parameters, chlorophyll fluorescence ki- netic parameters, chlorophyll content, relative soluble sugar content, malonaldehyde content, relative proiine content, relative conductivity and other 12 physiological indi- cators of seedling leaves under low temperature treatment (5 ℃, 12 h) and recovery treatment (25 ℃. 24 h) were determined; based on the chilling tolerance coefficient (CTC) of various individual indicators, the comprehensive evaluation of chilling toler- ance was conducled by using principal component analysis, hierarchical cluster anal- ysis and stepwise regression analysis. [Result] The results showed that the 12 indi- vidual physiological indicators could be classified into 7 independent comprehensive components by principal component analysis; 15 cotton varieties (lines) were clus- tered into three categories by using membership function method and hierarchical cluster analysis; the mathematical model for evaluating chilling tolerance of cotton seedlings was established: D =0.275 -0.244Fo1 +0.206Fv/Fm1+0.326g,%-0.056SS + 0.225MDA+O.O38REC (FF=0.995), and the evaluation accuracy of the equation was higher than 94.25%,0. Six identification indicators closely related to chilling tolerance were screened, including Fo,, Fv/Fm1, Seedling leaves of cotton varieties (lines) gs2, SS, MDA, and REC. [Conclusion] with high chilling tolerance are less dam- aged under low temperature stress, and are able to maintain relatively high photo- synthetic electron transport capacity and high stomatal conductance after recovery treatment, which is contributed to gas exchange and recovery of photosynthetic ca- pacity. Determination of the six indicators under the same stress condition can be adopted for rapid identification and prediction of the chilling tolerance of other cotton varieties, which provides basis for the breeding, promotion, identification and screen- ing of chilling tolerant germplasms.