Objective This study investigated the morphological and photosynthetic responses of the nationally certified cultivar ‘Shenqiu Hong’ of Hippophae rhamnoides under drought, saline-alkali, and combined drought-saline-alkali stresses.

Methods One-year-old clonal seedlings were used as the experimental material. Natural water deficit control and gradient saline-alkali irrigation were applied to establish treatments with different soil volumetric water contents, different saline-alkali concentrations, and combined stresses. Morphological changes were observed and photosynthetic parameters were measured.

Results (1) Drought stress, saline-alkali stress, and their combined stress suppressed morphological performance and photosynthetic function in H. rhamnoides seedlings, with the combined stress exerting markedly stronger effects than either single stress. (2) The effects of single stress were minimal at early stages but intensified with increasing stress duration and severity, leading to declines in chlorophyll content (SPAD), electron transport rate (ETR), light-use efficiency (α), and the maximum photochemical efficiency of PSII (F_v/F_m). Under combined stress, SPAD, ETR, and F_v/F_m were markedly reduced, accompanied by a concurrent decrease in PSII reaction center density (RC/CSo), resulting in impaired electron transport and constrained light energy absorption and trapping. (3) Under drought stress or saline-alkali stress, seedlings predominantly maintained photosystem stability by enhancing regulated non-photochemical energy dissipation Y(NPQ). In contrast, during the late stage of severe combined stress, Y(NPQ) declined sharply while non-regulated energy dissipation Y(NO) increased substantially, ultimately leading to functional destabilization of the photosynthetic apparatus. (4) Combined drought–salinity stress markedly altered the energy flux organization of the thylakoid membrane. With increasing stress intensity, the absorbed energy flux (ABS/CSm), trapped energy flux (TRo/CSm), and electron transport flux (ETo/CSm) all declined substantially, with reductions significantly greater than those observed under single-stress treatments. (5) High-intensity combined stress treatments clustered independently at the Per3–Per4 stages, clearly separated from single-stress conditions. PSII stability indices (F_v/F_m, RC/CSo) showed strong positive correlations with photochemical performance and electron transport metrics, and significant negative correlations with V_k, V_j, and Y(NO), indicating that the decline in PSII activity is accompanied by impaired electron transport at both the donor and acceptor sides and by enhanced non-regulated energy dissipation.

Conclusion Morphological and photosynthetic damage in H. rhamnoides indeced by combined stress are the most severe compared with individual drought or saline-alkali stresses. H. rhamnoides activates photoprotective mechanisms through enhanced thermal dissipation to mitigate stress damage under drought or saline-alkali conditions. However, these adaptions were compromised under combined stress, resulting in irreversible photodamage. The results enhance our understanding of stress adaptation in woody plants and serve as a reference for selecting and breeding tree species for ecological restoration in drought-and saline-alkali regions.