Photosystem II (PSII) is susceptible to photodamage under high light stress, necessitating an efficient repair cycle that involves the degradation of the damaged D1 protein, primarily by FtsH proteases. While the involvement of FtsH in D1 turnover is established, the regulatory mechanisms ensuring precise degradation remain unclear. In this study, we characterize the function of TEF6, a conserved thylakoid membrane protein with two transmembrane domains in Chlamydomonas reinhardtii. The tef6 exhibits severe growth inhibition, reduced PSII activity, impaired accumulation of PSII supercomplexes, and disorganized thylakoid membranes specifically under high light conditions. Physiological, cellular, biochemical and genetics assays confirmed that loss of TEF6 specifically impairs PSII stability and repair. Furthermore, multiple approaches including co-immunoprecipitation coupled with mass spectrometry, yeast two-hybrid assays, and bimolecular fluorescence complementation (BiFC) experiments demonstrated that TEF6 directly interacts with both the D1 protein and the FtsH proteases (FtsH1/FtsH2). Loss of TEF6 leads to misregulated, excessive accumulation of FtsH under high light, which correlates with accelerated and uncontrolled degradation of the D1 protein, ultimately disrupting the PSII repair cycle and homeostasis. Our findings identify TEF6 functioning as a crucial scaffold-like factor in the PSII repair machinery. TEF6 stabilizes the proper accumulation of the FtsH protease complex in the thylakoid membrane, thereby ensuring the correct and regulated turnover of photo-damaged D1. This study reveals a novel regulatory mechanism, mediated by a GreenCut protein, for maintaining PSII quality control and photosynthetic efficiency under light stress.