Abstract: The construction of the Yellow River Yangqu Hydropower Station necessitated the relocation of native Tamarix austromongolica in the reservoir area to higher elevations. To investigate the impact of transplantation on the photosynthetic physiology of T. austromongolica, chlorophyll fluorescence parameters were compared between a transplanted population (four years post-transplantation) and a native population in the reservoir area. The aim was to elucidate the effects of transplantation on the photosynthetic apparatus and identify key responsive indicators, providing a foundation for subsequent mechanistic research. The results showed that: (1) In the transplanted population, Y(NPQ) was significantly decreased, while Y(NO) was significantly increased compared to the native population, indicating reduced regulatory photoprotective capacity and an increased risk of photodamage. Significant decreases in qN and NPQ, a significant increase in F_o, and a significant decrease in F_v/F_m suggested mild photoinhibition. Furthermore, significant increases in F_j and M_o indicated impaired electron transport from QA to QB. (2) The first two principal components accounted for 81.7% of the total variance, with PC1 representing the overall metabolic load of PSII and PC2 reflecting PSII photochemical efficiency and electron transport dynamics. (3) Y(NPQ) showed a highly significant negative correlation with Y(NO) and highly significant positive correlations with qN and NPQ. Mo exhibited a highly significant negative correlation with F_v/F_m and a highly significant positive correlation with Y(NO), confirming the trade-off in energy partitioning and the coupling between impaired electron transport and decreased photochemical efficiency. (4) Although there are currently no significant differences in soil conditions between the transplanted and native areas, root damage during the transplantation process and its legacy effects may be the core drivers of the observed differences in photosynthesis. (5) F_v/F_m, M_o, and F_j can serve as sensitive indicators for diagnosing transplantation success. In the conservation of rare plants through transplantation in water conservancy projects in arid regions, high priority should be given to root protection during the transplantation process, and the causal relationship between root damage and photosynthetic recovery should be further validated through long-term dynamic monitoring.