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The planting of salt-tolerant plants is regarded as the one of important measurements to improve the saline–alkali lands. The outstanding biological properties of JUNCAOs have made them candidates to improve and utilize saline–alkali lands. At present, little attention has been paid to developing a non-destructive and high throughput approach to evaluate the salt tolerance of JUNCAO. To close the gaps, three typical JUNCAOs (A.donax. No.1, A.donax. No.5 and A.donax. No.10) were evaluated by combining prompt chlorophyll a fluorescence (ChlF) with hyperspectral spectroscopy (HS). The results showed that salt stress reduced relative stem growth, water content, and total chlorophyll content but enhanced the malondialdehyde (MDA) content. It caused a significant change in chlorophyll a fluorescence kinetics with an appearance of L-, K- and J-band, implying damaging energetic connectivity between PSII units, uncoupling of the oxygen evolving complex (OEC) and inhibition of the Q A −reoxidation. The negative impact of salt stress on JUNCAOs increased with the increasing level of salt concentration. Effect on spectral reflectance in the in the visible region with shifts on red edge position (REP) and blue edge position (BEP) to shorter wavelength was also found in salt stress plants. Combining principal component analysis (PCA) with the membership function method based on spectral indices and JIP-test parameters could well screen JUNCAOs salt tolerant ability with the highest for A.donax. NO.10 but lowest for A.donax. NO.1, which was the same as that of using conventional approach. The results demonstrate that prompt ChlF coupling with HS could provide potentials for non-invasively and high-throughput phenotyping salt tolerance in JUNCAOs. • Salt damaged energetic connectivity, oxygen evolving complex and Q A − reoxidation. • Salt induced shifts on red and blue edge positions to shorter wavelength. • Prompt ChlF and HS have potentials for high-throughput phenotyping salt tolerance. [ABSTRACT FROM AUTHOR]