Saline-alkali stress is a major environmental factor limiting plant growth. To investigate physiological response of Malus halliana to saline-alkali stress and screen the threshold of saline-alkali tolerance, the characteristics of photosynthetic pigments, chlorophyll fluorescence parameters and osmolytes were studies and multiple indices were analyzed by correlation analysis and principal component analysis (PCA). Two-year-old of M. halliana was employed as experiment materials, and 5 different concentrations of saline-alkali stress (0, 50, 100, 150, 200 mmol/L) were simulated on the basis of NaCl and NaHCO₃ (1:1) by pot experiment. The results showed that:with the increaseing of salt concentration, the chlorophyll content (Chl T), net photosynthesis (P_n), stomatal conductance (G_s), transpiration rate (T_r), intercellular CO₂ concentration (C_i), leaf water content (WC), maximal photochemical efficiency (F_v/F_m), photosynthetic electron transport rate (ETR), actual photochemical efficiency (φPSⅡ) and photochemical quenching coefficient (qP) were decreased, whereas the carotenoid content (Car), water use efficiency (WUE), electrolyte leakage rate and non regulatory energy dissipation (Y(NO)) were increased. After 40 d stress, the initial fluorescence (F₀) increased significantly but regulatory energy dissipation (Y(NPQ)) and non photochemical quenching coefficient (qN) decreased significantly. However, the content of proline, soluble sugar and total organic acid remarkablely accumulated and reached the maximum at salinity 100 mmol/L. The P_n of M. halliana had a positive relation with G_s, C_i, ETR, φPSⅡ, T_r, WC, qP and Chl T, while it correlated negatively with electrolyte leakage rate, proline and Y(NO). In summary, dynamic balance of photosynthetic system between injury and repair of M. halliana leaves was kept by reducing G_s, C_i, T_r and WC, increasing WUE, accumulating a large amount of osmotic regulators and starting heat dissipation mechanism under saline-alkali stress. Based on PCA, the concentration of 100 mmol/L was the critical threshold for saline-alkali tolerance. Moreover, the G_s, C_i, ETR, φPSⅡ, T_r, WC, qP and Chl T, electrolyte leakage rate, proline and Y(NO) could be used as effective indices to evaluate saline-alkali resistance. This study provided a theoretical basis for clarifying the critical threshold of saline-alkali tolerance in M. halliana.