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Green photosynthetic stems are often responsible for photosynthesis due to the reduction of leaves in arid and hot climates. We studied the response of PSII activity to high irradiance in the photosynthetic stems of Hexinia polydichotoma in the Taklimakan Desert by analysis of the fast fluorescence transients (OJIP). Leaf clips of a chlorophyll fluorometer were used in conjunction with a sponge with a 4-mm-width groove to prevent light leakage for precise in vivo measurements. High irradiance reduced performance indices, illustrating the photoinhibition of PSII to some extent. However, the decrease in active reaction centers (RC) per PSII absorption area and maximum quantum yield indicated a partial inactivation of RCs and an increase in excitation energy dissipation, resulting in downregulation of photosynthetic excitation pressure. In addition, the increased efficiency of electron transport to PSI acceptors alleviated overexcitation energy pressure on PSII. These mechanisms protected the PSII apparatus as well as PSI against damages from excessive excitation energy. We suggested that H. polydichotoma exhibited rather photoadaptation than photodamage when exposed to high irradiance during the summer in the Taklimakan Desert. The experiment also demonstrated that the modified leaf clip can be used for studying dark adaptation in a photosynthetic stem.