The aim of the study was to examine the role of root abscisic acid (ABA) in protecting photosystems and photosynthesis in Jerusalem artichoke against salt stress. Potted plants were pretreated by a specific ABA synthesis inhibitor sodium tungstate and then subjected to salt stress (150 mM NaCl). Tungstate did not directly affect root ABA content and photosynthetic parameters, whereas it inhibited root ABA accumulation and induced a greater decrease in photosynthetic rate under salt stress. The maximal photochemical efficiency of PSII (Fv/Fm) significantly declined in tungstate-pretreated plants under salt stress, suggesting photosystem II (PSII) photoinhibition appeared. PSII photoinhibition did not prevent PSI photoinhibition by restricting electron donation, as the maximal photochemical efficiency of PSI (ΔMR/MR0) was lowered. In line with photoinhibition, elevated H2O2 concentration and lipid peroxidation corroborated salt-induced oxidative stress in tungstate-pretreated plants. Less decrease in ΔMR/MR0 and Fv/Fm indicated that PSII and PSI in non-pretreated plants could maintain better performance than tungstate-pretreated plants under salt stress. Consistently, greater reduction in PSII and PSI reaction center protein abundance confirmed the elevated vulnerability of photosystems to salt stress in tungstate-pretreated plants. Overall, the root ABA signal participated in defending the photosystem’s photoinhibition and protecting photosynthesis in Jerusalem artichoke under salt stress.